The impact of river flooding and high flow on the demersal fish assemblages of the freshwater-dominated Great Fish Estuary,South Africa

Freshwater inflow has a strong impact on the biological, chemical and physical characteristics of estuaries, which in turn affect the distribution and abundance of estuarine organisms. Increased climatic variability associated with climate change is predicated to modify precipitation patterns, which will likely intensify floods in estuaries. The demersal fish assemblage of the freshwater-dominated Great Fish Estuary, South Africa, was sampled using beam trawls, monthly, from December 2013 to November 2014. The first six months of the study were characterised by river flooding and high flow, with estuarine conditions found only in the mouth region; this was followed by six months of intermediate flow, with estuarine conditions recorded up to 10 km from the mouth. River flooding and subsequent reduced salinity resulted in a decrease in species richness and abundances of fishes in the estuary, with only two estuarine species (Glossogobius callidus and Psammogobius knysnaensis) and one marine migrant (Solea turbynei) recorded following river flooding (201 m³ s^?1), in January 2014. The greatest species richness and abundances among both marine and estuarine fishes were recorded during intermediate flow conditions. We conclude that although freshwater inflow into estuaries is important for the nursery function of these systems, flooding—especially in freshwater-dominated estuaries—may cause a temporary decline in the abundance of most marine and estuarine fish species, including important bentho-pelagic marine migrant fishery species, such as Argyrosomus japonicus and Pomadasys commersonnii.     

Inter- and intra-estuarine fish assemblage variability patterns along the Portuguese coast

Estuaries along the Portuguese coast differ considerably in terms of their structure, geomorphologic and hydrologic characteristics. They play an important ecological role for different fish species, namely acting as important nursery areas. The fish assemblages of nine estuaries of the Portuguese coast were investigated in order to evaluate their main inter- and intra-estuarine variability patterns. Fish sampling surveys were conducted in May and July 2006, covering the full estuarine gradient. The different saline areas in each estuary were mapped using a Geographic Information System and fish assemblages’ were described and compared using a functional guilds approach. Generalized linear models were used to relate fish species richness to geomorphologic, hydrologic and environmental characteristics of the estuaries considered and correspondence analyses were performed to evaluate similarities in fish assemblages’ structure. At a large scale, river flow was the most important factor explaining the variability in species richness in estuaries along the Portuguese coast. At a regional scale, different abiotic factors explained the occurrence and abundance of fish species in the estuaries. Nonetheless, the overall role of the estuary was strongly related with the dominant saline zone within each estuary.     

Fish composition and assemblage structure in three Eastern English Channel macrotidal estuaries: A comparison with other French estuaries

This study has analysed for the first time fish composition and assemblage structures of three small macrotidal estuaries of the Eastern English Channel (EEC) and has explored the influences of 19 biotic and abiotic variables on the fish assemblages. Fish from Canche, Authie and Somme estuaries were collected during spring (June 2006 and May 2007) and autumn (September 2006) along the estuarine gradients using a 1.5 m beam trawl. Using identical sampling protocols, the study also analysed and compared for the first time taxonomic and functional aspects of the fish assemblages in 15 estuaries located along the Atlantic and English Channel coasts. SIMPER analysis showed high similarities in fish assemblages in the three EEC estuaries and during either spring or autumn periods. However, intra-estuary similarities were relatively low, indicating that fish assemblage structures (species richnesses or abundances) were more variable within the estuary (salinity gradient) than between estuaries and/or seasons (spring vs autumn). Although numerous environmental variables were included in the study, only 47% of the variability observed in the fish distribution was explained. Fish spatial variations in the EEC estuaries are mostly driven by abiotic variables as opposed to biological interactions. As indicated by CCA, salinity and muddy sediments were the two most important factors structuring the fish assemblages. The macrobenthos being very abundant in the EEC estuaries (580–1121 ind. m⁻²), the availability of potential prey is probably not a limiting factor in the utilization of estuaries by fish. Contrary to the majority of French estuaries dominated by estuarine species (ES), the fish assemblages of the EEC estuaries are clearly dominated by marine migrant (MM) species (65% on average) with high abundance of juveniles (mostly young-of-the-year). Cluster and SIMPROF's analyses distinguished the functional structure of the 15 estuarine fish assemblages into different clusters. The three EEC estuaries form a similar group with the largest French estuaries (Seine, Loire and Gironde). The latters were characterized by higher MM/ES ratio compared to the other French estuaries. Freshwater flow and tidal range were the main factors associated with this group of estuaries. The results of the present study do not indicate that anthropogenic impacts (chemical contamination) on estuaries affect their ecological functioning as described by the fish ecological guilds. It is suggested that the guild approach may not be useful to provide valuable information on the ecological status of estuaries.     

Spatial variation in elemental composition of otoliths of three species of fish (family Sparidae)

Determining the nursery habitat of fishes that have moved from estuarine nursery habitats is difficult. The elemental fingerprints of otoliths of three species of sparids were determined to investigate their utility as a natural tag of the nursery habitat. Juvenile Pagrus auratus (snapper), Rhabdosargus sarba (tarwhine) and Acanthopagrus australis (bream) were collected from two sites in each of 15, six and three estuaries, respectively, and their otoliths analysed by solution-based inductively coupled plasma-mass spectrometry. Significant differences in otolith chemistry were found for all three species of juveniles collected from different estuaries. The same patterns among estuaries were not seen for all species, although it was not possible to sample the same sites within an estuary for all species. For bream, significant differences in otolith chemistry were found among all three estuaries, whereas for tarwhine the six estuaries were separated into three groups. For snapper, a number of estuaries could be separated, but there was some overlap for other estuaries. All three species were collected from the same site within one estuary and their otoliths analysed. Significant differences were found among species, but the implication of this finding remains unclear as the three species show differences in microhabitat use and may also differ in age. Because the elemental fingerprints of juveniles vary among estuaries or groups of estuaries, the nursery or recruitment estuary of adult fish could now be determined by analysing the juvenile region of adult otoliths. Thus, connectivity between estuaries and open coastal populations could be determined. Such information will have major implications for fisheries management because it will provide information on the distance that fish have moved from their recruitment estuary and the number of estuaries that contribute to each adult population.     

The impact of extreme turbidity events on the nursery function of a temperate European estuary with regulated freshwater inflow

Estuaries are used as nursery grounds by numerous marine species despite being usually subject to strong anthropogenic disturbances. Abundances of marine recruits (fish and crustacean decapods) and their main prey (mysids) were monitored by monthly sampling, from June 1997 to February 2009, in the lower reaches of the Guadalquivir estuary (SW Spain). During that period, unusually high and persistent turbidity events (HPTEs) were observed twice. Both HPTEs started with strong and sudden freshwater discharges after relatively long periods of very low freshwater inflow. Data from this time-series were used to test the hypothesis that HPTEs may negatively impact the nursery function of estuaries either by decreasing prey availability or by decreasing survival/arrival of marine recruits. During HPTEs, the commonest mysid (Mesopodopsis slabberi), a key species in the estuarine food web, showed a significant decrease in abundance. Likewise, some marine recruits that prey on M. slabberi and whose peaks of abundance within the estuary occur in summer–autumn (Engraulis encrasicolus and Pomadasys incisus) were less abundant during HPTEs. It is also suggested that HPTEs might have triggered a shift in the distribution of the most euryhaline prey (Neomysis integer) and predator (Dicentrarchus punctatus and Crangon crangon) species, towards more saline waters. This could have contributed to an increase in the inter-specific competition (for food/habitat) within the estuarine nursery area. The results discussed in this study call attention to the need to reduce as much as possible the anthropogenic pressures that may stimulate the occurrence of high and persistent turbidity events (HPTEs) in order to preserve the nursery function of temperate estuaries.     

The importance of estuary head waters as nursery areas for young estuary- and marine-spawned fishes in temperate South Africa

The restriction of freshwater flow into estuaries, the presence of in-stream barriers and the occurrence of invasive fish species in these habitats are identified as major threats to these young estuary- and marine-spawned fish species. These aspects have been investigated using the distribution and abundance of young estuary- and marine-spawned fish species in the headwater environments of four permanently open estuaries of the Eastern Cape, South Africa. Fishes were collected twice per season over the 2009 and 2010 period, using mixed method sampling with seine net hauls and overnight fyke net deployments. Of the 74,751 fishes collected, 37,444 fishes, 18 families and 34 species were taken in fyke net catches, while 34,308 fishes, 21 families and 38 species were caught in seine nets. In the Great Fish, Kowie, Kariega and Sundays River systems, juveniles of estuarine residents dominated headwater catches, followed by juveniles of estuary-dependent marine species. The prevalence of larval and small juvenile stages of estuary- and marine-spawned fish species highlights the potential importance of these transitional areas for young fish.     

Nursery use patterns of commercially important marine fish species in estuarine systems along the Portuguese coast

Analysing the estuarine use patterns of juveniles of marine migrant fish species is vital for identifying important sites for juveniles as well as the basic environmental features that characterize these sites for different species. This is a key aspect towards understanding nursery function. Various estuarine systems along the Portuguese coast (Minho, Douro, Ria de Aveiro, Mondego, Tejo, Sado, Mira, Ria Formosa and Guadiana) were sampled during Spring and Summer 2005 and 2006. Juveniles of commercially important marine fish species Solea solea, Solea senegalensis, Platichthys flesus, Diplodus vulgaris and Dicentrarchus labrax, predominantly 0-group individuals, were amongst the most abundant species and had distinct patterns of estuarine use as well as conspicuous associations with several environmental features. Juvenile occurrence and density varied amongst estuaries and sites within them, and differed with species. Sites with consistently high juvenile densities were identified as important juvenile sites (i.e. putative nursery grounds). Through generalized linear models (GLM), intra-estuarine variation in occurrence and density of each of the individual species was largely explained by environmental variables (temperature; salinity; depth; percentage of mud in the sediment; presence of seagrass; importance of intertidal areas; relative distance to estuary mouth; macrozoobenthos densities; and latitude). Decisive environmental factors defining important sites for juveniles varied depending on the system as a result of different environmental gradients, though there were common dominant features for each species regardless of the estuary considered. Analysed environmental variables in the GLM also accounted for inter-estuarine variation in species' occurrence and density. In several estuaries, the identified important juvenile sites were used by many of these species simultaneously and may be of increased value to both management and conservation. Overall, the variability in site features amongst estuaries highlighted the tolerance of these species to different available environmental conditions and provided fundamental information for future spatially explicit modelling of their distribution. This should ultimately enable the prediction of species response to habitat alterations.     

Quality of coastal and estuarine essential fish habitats: estimations based on the size of juvenile common sole (Solea solea L.)

Survival and growth of early fish stages are maximal in coastal and estuarine habitats where natural shallow areas serve as nurseries for a variety of widely distributed species on the continental shelf. Processes occurring in these nursery grounds during the juvenile stage affect growth and may be important in regulating the year-class strength of fishes and population size. The need, therefore, exists to protect these essential fish habitats hence to develop indicators to estimate their quality.The purpose of the present study was to use the growth of juvenile sole as a means of comparing the quality of coastal and estuarine nursery habitats in the Bay of Biscay (France). These sole nurseries were clearly identified from studies based on trawl surveys carried out during the last two decades. The size of 1-group juveniles at the end of their second summer, as estimated from these surveys, is an indicator of growth in these habitats during the juvenile phase and can be used to compare habitat quality. A model taking into account the role of seawater temperature in spatial and interannual variations of juvenile size was developed to compare growth performance in the different nursery sectors.This study shows that the size of juvenile sole after two summers of life is not density-dependent, probably because the size of the population adapts to habitat capacity after high mortality during early-juvenile stages. Size is on one hand positively related to temperature and on the other hand higher in estuarine than in non-estuarine habitats. This high growth potential of juvenile fish in estuarine areas confirms the very important role played by estuaries as nursery grounds and the essential ecological interest of these limited areas in spite of their low water quality. If a general conclusion on habitat quality is to be reached about studies based on the growth of juvenile fish, it is necessary to use not only an integrative indicator of growth, like size, representative of the intrinsic habitat quality, but also more sensitive and less integrative means, such as otolith increments or caging experiments, which better respond to anthropogenic disturbance. Moreover, it is necessary to take juvenile densities into account.     

Dynamics of recruitment of larval and juvenile Cape stumpnose Rhabdosargus holubi (Teleostei: Sparidae) into the Swartkops and Sundays estuaries,South Africa

Recruitment of early life stages into estuaries is an integral part of the life cycle of many marine fish species. Although estuaries are naturally environmentally dynamic, they also are subject to anthropogenic disturbances, including land use and climate change, which may affect recruitment. Rhabdosargus holubi is an endemic marine-spawning species predominantly associated with freshwater-rich estuaries which serve as nursery areas for postflexion larvae and juveniles. This study assessed the effect of environmental variables on the dynamics of recruitment of R. holubi larvae and juveniles into the Swartkops and Sundays estuaries, South Africa. Over a period of two years, fyke nets were set at each estuary mouth to monitor movement into the estuaries at each tidal phase over a 24 h cycle during two sampling sessions per season. Rhabdosargus holubi larvae recruited into estuaries primarily in summer and autumn and during the ebb tide at night, while juvenile movements showed no pattern. Salinity, turbidity and temperature were significantly important factors affecting R. holubi recruitment, with pH having no significant effect. Turbidity and salinity are affected by rainfall and freshwater abstraction which may thus influence recruitment. Rhabdosargus holubi is dependent on estuaries, so a combination of future changes in turbidity, salinity and temperature due to predicted climate change may place populations at risk.     

Environmental factors structuring fish composition and assemblages in a small macrotidal estuary (eastern English Channel)

The fish assemblage structure was analyzed along an estuarine gradient of a small macrotidal estuary (the Canche, France). Fishes were collected every two months between May 2006 and July 2007 from 12 sampling stations using a 1.5-m beam trawl with a 5 mm mesh size in the cod end. To complement this information, sampling was also performed using 15-m fyke nets (8 mm mesh size in the cod end). For each sample, abiotic (temperature, salinity, pH, oxygen, turbidity, river flow, wind speed and depth) and biotic (macro crustacean species abundances) were recorded. Throughout the study, 28 fish species belonging to 20 families were collected. Fish catches were dominated by juveniles, especially Young-Of-the-Year (YOY) for the majority of the species. According to the Index of Relative Importance (IRI), common goby Pomatoschistus microps, flounder Platichtys flesus, sprat Sprattus sprattus, sea-bass Dicentrarchus labrax and plaice Pleuronectes platessa were the most abundant species, together accounting for 99.2% of the total IRI. Estuarine residents (ER = 66.2%) and marine juvenile migrants species (MJ = 31.4%) were the most important ecological guilds. The structure of the fish assemblage and its relationship to environmental variables was examined using multivariate techniques. Cluster and non-metric multidimensional scaling (nMDS) analysis defined six distinct groups in the Canche estuary, which are discriminated by specific species (SIMPER). Spatio-temporal variations in fish assemblage structure reflect the density peaks of the most abundant species. Spearman rank correlations and canonical correspondence analysis (CCA) showed that among the ten environmental variables examined, temperature, salinity and Crangon crangon (a potential predator for YOY fish or prey for older ones) are the three most important factors influencing fish species richness and abundances. Our observations reinforce the idea that certain fish species may have different life history styles in different geographic areas. The present study highlights the necessity of a better knowledge of the connectivity between estuaries and adjacent marine areas. The Canche constitutes an important ecosystem for fishes and as it is subject to little anthropogenic disturbance; its ichthyofauna can be viewed as a reference or normal assemblage for small temperate macrotidal estuaries.     

Fish Assemblages in Shallow Marine Caves of the Salento Peninsula (Southern Apulia, SE Italy)

Abstract. Fish assemblages of three shallow marine caves from the Salento Peninsula (Apulia, SE Italy) were investigated in July 2000. Data were collected in situ by using visual census. A total of nineteen fish species were recorded inside the caves. The species richness generally displayed a similar pattern in all three caves, decreasing from the entrance towards the innermost sections, whereas the patterns of total fish abundance differed among caves. Apogon imberbis (mainly represented by juveniles) was the most important species in terms of number of individuals (accounting for more than 85% of the censused fish) and showed a fairly even distribution inside the investigated caves. Without the numerical contribution of A. imberbis , fish abundance decreased from the entrance to the inner sections and this pattern was common to all three caves. Juvenile fishes of economic interest ( e. g., Diplodus vulgaris and Epinephelus marginatus ) were also recorded inside. The present study suggests that: (1) environmental constraints could affect distribution patterns in fish species richness and in the abundance of several fish along the axis of "blind caves" (with a single entrance), as already observed for sessile benthos and plankton assemblages; (2) shallow marine caves of the Salento Peninsula could exert the role of refuge and/or nursery for some littoral fish species during the adult and/or juvenile stages of their life histories.     

Habitat utilization by fishes in a shallow, semi-enclosed estuarine bay in southern Gulf of Thailand

One hundred and eight fish species were collected between March 2003 and February 2004 from 11 study sites in Pattani Bay, southern Gulf of Thailand. The catches consisted primarily of juveniles or adults of small-sized fishes, indicating that the bay was important as nursery ground for fishes. Of the 43 families, Leiognathidae (43.3% contribution), Centropomidae (15.2%), Siganidae (13.8%), Engraulidae (10.3%), Atheriniidae (6.9%), Clupeidae (4.8%) and Ariidae (3.1%) were dominant in the catch. Significant differences were found in relative abundance and species richness between both sampling sites and months. The sampling sites were clearly defined by fish community into four different habitats that were directly related with the bottom structure of each site. The 30 most dominant fish species were categorized according to habitat preference into five different groups. Some species exhibited preference for specific habitats, whereas others were distributed throughout the bay. Seasonally, fish community structure revealed four different recruitment and occurrence periods, which were February to April, May to September, October and November to January, which was partially related to local monsoonal seasons. Analysis of the 30 most dominant fish species demonstrated that they were clustered into six different seasonal groups, with some showing a clear preference for specific months, although many recruited and occurred throughout the year. Results of this study help to clarify the ranges of habitats, months and seasons used by a number of fish species found in tropical coastal habitat.     

Fish utilization of a salt marsh intertidal creek in the Yangtze River estuary, China

The structure and temporal variations of the fish community in salt marshes of Chinese estuaries are poorly understood. Fish utilization of a salt marsh intertidal creek in the Yangtze River estuary was studied based on quarterly sampling surveys in July and November, 2004, and February and May, 2005. Fishes were collected by consecutive day and night samplings using fyke nets during the ebbing spring tides. A total of 25,010 individuals were caught during the study. 17 families and 33 species were documented, and the most species-rich family was Gobiidae. Three species, Synechogobius ommaturus, Chelon haematocheilus and Lateolabrax maculatus together comprised 95.65% of the total catch, which were also the most important commercial fishery species in the Yangtze River estuary. The fish community was dominated by juvenile individuals of estuarine resident species. Time of year significantly affected fish use of salt marshes, but no significant effects of diel periodicity on the fish community were found except for fish sampling in July. These findings indicate that salt marshes in the Yangtze River estuary may play important nursery roles for fish community.     

Ichthyoplankton in a southern african surf zone: Nursery area for the postlarvae of estuarine associated fish species?

The surf zone ichthyoplankton of Swartvlei Bay was studied between February 1986 and June 1987, with particular emphasis on its potential role as a nursery area for estuarine associated marine fish species. Larvae and/or postlarvae of 16 families were identified from the surf zone, with the Gobiidae, Soleidae, Sparidae and Mugilidae comprising 85·7% of all teleosts sampled. The postlarvae of several taxa (including the six most common species), which utilize the Swartvlei estuary as a juvenile nursery area, were abundant in the surf zone. Conversely, species which are common in nearshore marine waters as juveniles and adults, but seldom enter estuaries, totalled less than 8% of the surf zone ichthyoplankton assemblage.Larval and postlarval densities peaked during summer when water temperatures exceeded 19°C and the estuary mouth was open. Concentrations of ichthyoplankton were highest at those sampling stations closest to the estuary mouth during the summer period. Diel changes in total catches revealed no significant difference between day and night densities; but of the four major taxa, the Mugilidae and Sparidae tended to be more abundant during the day, the Gobiidae at night and the Soleidae showed no distinct pattern. Results from a 24 h sampling session indicated that tidal phase may also be important in governing ichthyoplankton abundance in the surf zone.     

Factors Influencing Fish Composition in an Australian Intermittently Open Estuary. Is Stability Salinity-Dependent?

The ichthyofauna of the intermittently open Shellharbour Lagoon in southeastern Australia was sampled over 14 months to investigate factors influencing species composition. Zostera capricorni and bare sand habitats were sampled every two months with a fine-mesh seine. Of the 10 277 fish caught representing 19 families and 27 species, the most numerically dominant species were Pseudogobius olorum and Pseudomugil signifer. The most abundant economically important species were Acanthopagrus australis, Mugil cephalus and Myxus elongatus. Mean number of fish and species was significantly higher over Zostera than bare sand during months immediately after the estuary opened when juvenile marine fishes recruited, demonstrating the estuary's nursery function. In contrast to other intermittently open estuaries in Australia and South Africa, Shellharbour Lagoon's fish assemblage appears resilient to perturbation and does not undergo distinct seasonal variations. This may be a result of the estuary's short open phases providing less opportunity for marine fishes to enter. Perhaps more importantly, the less dramatic fluctuations in salinity between open and closed phases maintains salinity at a level intermediate of the tolerances of both marine and estuarine fishes.     

Juvenile fish condition in estuarine nurseries along the Portuguese coast

Connectivity between estuarine fish nurseries and coastal adult habitats can be affected by variations in juvenile growth and survival. Condition indices are renowned proxies of juvenile nutritional status and growth rates and are valuable tools to assess habitat quality. Biochemical (RNA:DNA ratio) and morphometric (Fulton's condition factor K) condition indices were determined in juveniles of Solea solea, Solea senegalensis, Platichthys flesus, Diplodus vulgaris and Dicentrarchus labrax collected in putative nursery areas of nine estuaries along the Portuguese coast (Minho, Douro, Ria de Aveiro, Mondego, Tejo, Sado, Mira, Ria Formosa and Guadiana) in the Spring and Summer of two consecutive years (2005 and 2006) with distinct climatic characteristics. Individual condition showed significant variation amongst species. The combined use of both condition indices highlighted the low correlation between them and that RNA:DNA had a higher sensitivity. RNA:DNA varied between years but overall the site relative patterns in condition were maintained from one year to the other. Higher RNA:DNA values were found in Spring than in Summer in most species. Intra-estuarine variation also occurred in several cases. Species specific trends in the variability of condition amongst estuaries were highlighted. Some estuaries had higher juvenile condition for more than one species but results did not reveal an identical trend for all species and sites, hindering the hypotheses of one estuarine nursery promoting superior growth for all present species. Significant correlations were found between condition indices, juvenile densities and environmental variables (water temperature, salinity and depth) in the estuarine nurseries. These influenced juvenile nutritional condition and growth, contributing to the variability in estuarine nursery habitat quality. Management and conservation wise, interest in multi-species approaches is reinforced as assessments based on a single species may not reflect the overall nursery habitat quality.     

What makes mangroves attractive to fish? Use of artificial units to test the influence of water depth,cross-shelf location,and presence of root structure

Mangroves are an attractive fish habitat because they provide shelter and food for juvenile fishes. However, because mangroves are almost always located in shallow water and in sheltered (i.e., lagoonal, estuarine or bay) environments, the degree to which the latter two factors contribute to the attractiveness of mangrove prop-roots as a fish habitat is unknown. Artificial Mangrove Units (AMUs) were placed at multiple depths and along a gradient from an embayment to, and including, the coral reef. Total fish density and species richness in AMUs placed in the embayment was lower at 1 m depth than at 2 and 3 m depth, suggesting that shallow water is not a prerequisite for the attractiveness of mangrove prop-roots as a fish habitat. Total fish density and species richness were equal or greater in AMUs on the coral reef than in the embayment, suggesting that placement of mangroves in a sheltered lagoonal environment is not solely responsible for the attractiveness of mangrove prop-roots either. After 3 weeks, removal of AMUs did not have a negative effect on total fish density or species richness. However, within the embayment AMU removal resulted in the complete collapse of the assemblage component comprised of species that use mangroves as juvenile habitats, highlighting the need for a species-based approach towards assessing the benefits provided by the presence of mangrove root structure for fishes.     

What role do beds of submerged macrophytes play in structuring estuarine fish assemblages? Lessons from a warm-temperate South African estuary

Habitat variability is one of the factors influencing species richness within estuarine systems, and a loss of habitat can result in a restructuring of the estuarine ichthyofaunal assemblage, particularly if these conditions persist over long time periods. The potential effects of the loss of extensive submerged macrophyte beds (Ruppia cirrhosa and Potamogeton pectinatus) on an estuarine fish assemblage were investigated through an analysis of a long-term seine net catch dataset from the temporarily open/closed East Kleinemonde Estuary, South Africa. Catch data for a 12-year period, encompassing six years of macrophyte presence and six years of macrophyte senescence, indicated that the loss of this habitat did not influence species richness but changes in the relative abundance of certain species were evident. A shift in dominance from vegetation-associated species to those associated with sandy environments (e.g. members of the family Mugilidae) was observed. However, species wholly dependent on macrophytes such as the critically endangered estuarine pipefish Syngnathus watermeyeri were only recorded during years when macrophyte beds were present, while vegetation-associated species such as the sparid Rhabdosargus holubi persisted at lower levels of relative abundance. The reduced abundance of all vegetation-associated fish species during years of macrophyte senescence was probably reflective of declining food resources resulting from the loss of macrophyte beds and/or increased vulnerability to predation. Submerged beds of aquatic plants are therefore important habitats within temporarily open/closed estuaries, South Africa’s dominant estuary type.