Community structure of macrozooplankton in Trinity and Upper Galveston Bays

Macrozooplankton were sampled bi-weekly from October 1969 through May 1973 at 16 stations. Hydrological measurements, including water temperature and conductivity, accompanied each biological sample. Sampling sites and species were grouped by cluster analysis using Camberra-Metric measure of dissimilarity and flexible sorting. Two major seasons, based on taxon composition and abundance, were identified: A warm season (average water temperature above 22°C) dominated by larval and juvenile crustaceans, and a cool season with an abundance of larval fishes. Sites were more similar to each other within a year than they were between years. Differences between years correlated with variations in salinity and temperature. Community structure indices (Shannon-Weaver diversity, species richness and “evenness”) were applied to the seasonal data. Shannon diversity and “evenness” were positively correlated with each other, but richness values were often negatively correlated with the other two indices.     

Fish community ecology in an Altered River delta: Spatial patterns in species composition, life history strategies, and biomass

We sampled nearshore fishes in the Sacramento-San Joaquin Delta, California, United States, during 2001 and 2003 with beach seines and gill nets. We addressed three questions. How and why did fish assemblages vary, and what local habitat features best explained the variation? Did spatial variation in assemblages reflect greater success of particular life history strategies? Did fish biomass vary among years or, across habitats? Nonmetric multidimensional scaling showed that habitat variables had more influence on fish assemblages than temporal variables. Results from both gear types indicated fish assemblages varied between Sacramento and San Joaquin River sampling sites. Results from gill net sampling were less pronounced than those from beach seine sampling. The Sacramento and San Joaquin river sites differed most notably in terms of water clarity and abundance of submerged aquatic vegetation (SAV), suggesting a link between these habitat characteristics and fish relative abundance. Among-site differences in the relative abundance of periodic and equilibrium strategist species suggested a gradient in the importance of abiotic versus biotic community structuring mechanisms. Fish biomass varied among years, but was generally higher in SAV-dominated habitats than the turbid, open habitats in which we found highest abundances of striped bassMorone saxatilis and special-status native fishes such as delta smeltHypomesus transpacificus, Chinook salmonOncorhyncus tschawytscha, and splittailPogonichthys macrolepidotus. The low abundance of special-status fishes in the comparatively productive SAV-dominated habitats suggests these species would benefit more from large-scale restoration actions that result in abiotic variability that mirrors natural river-estuary habitat than from actions that emphasize local (site-specific) productivity.     

Nekton habitat quality at shallow water sites in two Rhode Island coastal systems

We evaluated nekton habitat quality at 5 shallow-water sites in 2 Rhode Island systems by comparing nekton densities and biomass, number of species, prey availability and feeding, and abundance of winter flounderPseudopleuronectes americanus. Nekton density and biomass were compared with a 1.75-m² drop ring at 3 sites (marsh, intertidal, and subtidal) in Coggeshall Cove in Narragansett Bay and two subtidal sites (eelgrass and macroalgae) in Ninigret Pond, a coastal lagoon. We collected benthic core samples and examined nekton stomach contents in Coggeshall Cove. We identified 16 species of fish, 16 species of crabs, and 3 species of shrimp in our drop ring samples. A multivariate analysis of variance indicated differences in total nekton, invertebrates, fish, and winter flounder across the five sites. Relative abundance of benthic invertebrate taxa did not match relative abundance of prey taxa identified in the stomachs. Nonmetric multidimensional scaling plots showed groupings in nekton and benthic invertebrate prey assemblages among subtidal, intertidal, and marsh sites in Coggeshall Cove. Stepwise multiple regression indicated that biomass of macroalgae was the most important variable predicting abundance of nekton in Coggeshall Cove, followed by elevation and depth. In Rhode Island systems that do not experience chronic hypoxia, macroalgae adds structure to unvegetated areas and provides refuge for small nekton. All sites sampled were characterized by high abundance and diversity of nekton pointing to the importance of shallow inshore areas for production of fishes and decapods. Measurements of habitat quality should include assessment of the functional significance of a habitat (this can be done by comparing nekton numbers and biomass), some measure of habitat diversity, and a consideration of how habitat quality varies in time and space.     

Distribution and community structure of ichthyoplankton in Laguna Madre Seagrass meadows: Potential impact of seagrass species change

Seasonal ichthyoplankton surveys were made in the lower Laguna Madre, Texas, to compare the relative utilization of various nursery habitats (shoal grass,Halodule wrightii; manatee grass,Syringodium filiforme; and unvegetated sand bottom) for both estuarine and offshore-spawned larvae. The species composition and abundance of fish larvae were determined for each habitat type at six locations in the bay. Pushnet ichthyoplankton sampling resulted in 296 total collections, yielding 107,463 fishes representing 55 species in 24 families. A broad spectrum of both the biotic and physical habitat parameters were examined to link the dispersion and distribution of both pre-settlement and postsettlement larvae to the utilization of shallow seagrass habitats. Sample sites were grouped by cluster analysis (Ward’s minimum variance method) according to the similarity of their fish assemblages and subsequently examined with a multiple discriminant function analysis to identify important environmental variables. Abiotic environmental factors were most influential in defining groups for samples dominated by early larvae, whereas measures of seagrass complexity defined groups dominated by older larvae and juveniles. Juvenile-stage individuals showed clear habitat preference, with the more shallowHalodule wrightii being the habitat of choice, whereas early larvae of most species were widely distributed over all habitats. As a result of the recent shift of dominance fromHalodule wrightii toSyringodium filiforme, overall reductions in the quality of nursery habitat for fishes in the lower Laguna Madre are projected.     

Settlement and Recruitment Patterns of the Soft-Shell Clam, <Emphasis Type="Italic">Mya arenaria</Emphasis>, on the Northern Shore of the Bay of Fundy,Canada

To examine the roles of settlement and early postsettlement processes in the recruitment of the soft-shell clam, Mya arenaria, abundance of recent settlers and juveniles was monitored over two field seasons at four locations on the northern shore of the Bay of Fundy in New Brunswick, Canada. Results showed great spatial and temporal variability in patterns of settlement. M. arenaria appeared to become highly vulnerable to postsettlement processes at a shell length of approximately 2 mm. Postsettlement processes drastically altered patterns of settlement less than 1 year after they were established. Results suggest that local factors at specific sites within the Bay of Fundy, such as hydrodynamics, larval behavior, and early postsettlement events, likely control the abundance of juvenile clams. Additionally, postsettlement events are extremely important in shaping M. arenaria populations in this area. Very few mature adult clams greater than 50 mm in shell length were found at any sampling sites, and no relationship was found between abundance of setters and density of juveniles and adults.     

Variation with Depth in Temperate Seagrass-Associated Fish Assemblages in Southern Victoria,Australia

Variability in the abundance and distribution of seagrass-associated fish assemblages was examined at different depths in a temperate bay in southern Australia. Depth differences in seagrass-associated fish assemblages are poorly known but this information is critical given that seagrass loss can occur at specific depths depending on the cause. Overall, 69 species of fish from 26 families were recorded, with higher species richness in shallow than deep beds, with 12 species found only in deep beds and 22 species found only in shallow beds. While the total fish abundance (i.e. abundance of all species recorded) varied between years and seasons, and to some extent between sites, it was significantly higher in shallow than deep seagrass beds in the majority of cases. Although there was some variation between sites, seagrass tended to be longer and have a higher biomass in shallow than deep beds during both spring and autumn throughout the study. A positive relationship between seagrass biomass/length and total fish abundance/species richness was apparent. Assemblage structure tended to be distinct at each depth, with the largest species recorded in shallow seagrass. Large numbers of small schooling fish, such as atherinids, dominated in shallow seagrass but were not found in deep seagrass. Loss of seagrass could therefore have varying implications for distinct assemblages found at different depths.     

Posthurricane Recovery of Riverine Fauna Reflected in the Diet of an Apex Predator

Hurricane Charley, a category 4 storm on the Safford–Simpson scale, passed over the Peace River, Florida, and its watershed on 13 August 2004 causing widespread hypoxia. An electrofishing study investigating the abundance of the euryhaline Centropomus undecimalis (common snook) began in the freshwater portions of the Peace River 3 months after the storm (November 2004) and included diet sampling. Samples were taken seasonally up to August 2006. Changes in the prey assemblages of C. undecimalis determined through multivariate analyses (e.g., nonmetric multidimensional scaling) were used as a proxy to estimate the recovery of riverine fauna. The initial posthurricane prey assemblages were dominated by species well adapted to low dissolved oxygen, namely Gambusia holbrooki and Hoplosternum littorale. A significant long-term serial change in assemblage structure occurred as the abundance of G. holbrooki and H. littorale decreased and other river fauna such as Procambarus spp. and ictalurid catfish increased. Assemblages were presumed as recovering 1 year after hurricane landfall, a posthurricane recovery period that is an order of magnitude longer than those reported for estuarine fish assemblages. The approach of using stomachs as sampling tools detected changes at the assemblage level that included an armored catfish species (e.g., H. littorale) and cryptic invertebrate species (e.g., Procambarus spp.) that went unnoticed in a study using standard electrofishing methods. Although sampling the diet of C. undecimalis was useful in detecting assemblage-level changes, other metrics—such as changes in health, sex ratio, relative abundance, and juvenile year-class strength of fishes and invertebrates collected by traditional fishing methods—are needed to fully evaluate the effects of the hurricane. Nonetheless, this study demonstrates that diet studies can supplement standard fishery gear to create a more comprehensive sampling strategy for aquatic fauna.     

Spring and Summer Larval Fish Assemblages in the Surf Zone and Nearshore off Northern New Jersey,USA

Larval fish use of surf zone and nearshore habitats at northern latitudes has received little attention. Consequently, potential impacts of beach nourishment and other forms of disturbance are not well understood. This study, on a northwestern Atlantic coastline spanning May through July over 4 years, demonstrates that recently hatched larvae are common in both surf zone and nearshore habitats. Taxonomic compositions of surf zone and nearshore assemblages were similar to each other and those from an adjacent estuary. An influence of upwelling events was apparent in coincident changes in abundance and/or size of several species in the surf zone. Other changes over the late spring–summer transition, including buoyancy-driven flows from the Hudson River plume, demonstrate the dynamic nature of larval fish assemblages in the New York Bight area.     

Diel Variation in the Pelagic Fish Assemblage in a Temperate Estuary

The pelagic fish assemblage within a temperate estuary was examined to determine if there were diel differences in species richness, total abundance, biomass, and species composition. These comparisons were made over both seasonal (January–December 1996) and annual (August–November 1995; August–December 1996) scales with pop net collections in a shallow (<2 m MLW) embayment within Great Bay in southern New Jersey, USA. In the complete year of sampling in 1996, more than 335,000 pelagic fish, representing 13 families (23 species), were collected during diel sampling with 12 species constituting over 99.9% of the total catch including Clupea harengus (84%), Menidia menidia (10%), and Anchoa mitchilli (4%). A detailed examination determined that nighttime species richness, total abundance and biomass may have been enhanced during some seasons by using artificial light. Diel variation in species composition was similar regardless of the use of the artificial light in all seasons but fall. Annual comparisons between 1995 and 1996 during late summer and fall found these results to be consistent. In general, these findings point out the importance of sampling during both day and night to understand the movement and abundance patterns of estuarine pelagic fishes and their ecological significance in temperate estuaries.     

The utilization of an intertidal salt marsh creek by larval and juvenile fishes: Abundance,diversity and temporal variation

The utilization of an intertidal salt marsh creek in South Carolina during January 1977 was determined by sampling every third ebb tide for 13 days. All fishes leaving the creek during that period were captured in a channel net. This procedure produced a time-series of samples which permitted analysis of the fish community occupying the intertidal creek at all times of day and night. A total of 14,730 larval, juvenile, and adult fishes comprising at least 22 species in 16 families were collected. The most common larval and juvenile fishes wereLeiostomus xanthurus, Mugil spp.,Myrophis punctatus leptocephali,Lagodon rhomboides, Paralichthys spp., andMicropogon undulatus. Catch sizes for all species varied widely between samples. No diurnal-nocturnal pattern in catches was evident forL. xanthurus, Mugil spp.,L. rhomboides andM. undulatus. M. punctatus was taken in large numbers only when the flood tide occurred during the day, while moreParalichthys spp. larvae were taken in late afternoon-evening flood tide samples. The most common invertebrate,Palaemonetes pugio, was taken in large quantities only in late afternoon-night flood tide samples. Three diversity indices were computed for each sample. Values for all indices varied widely between successive samples. The results emphasize a high degree of utilization of the intertidal creek habitat by larval and juvenile fishes. The diurnal-nocturnal activity patterns of some species, and the wide variation in catch size of the other species can permit use of the intertidal salt marsh habitat with reduced competition for available space and energy.     

Shoreline Hardening Affects Nekton Biomass,Size Structure,and Taxonomic Diversity in Nearshore Waters,with Responses Mediated by Functional Species Groups

Coastal shoreline hardening is intensifying due to human population growth and sea level rise. Prior studies have emphasized shoreline-hardening effects on faunal abundance and diversity; few have examined effects on faunal biomass and size structure or described effects specific to different functional groups. We evaluated the biomass and size structure of mobile fish and crustacean assemblages within two nearshore zones (waters extending 3 and 16 m from shore) adjacent to natural (native wetland; beach) and hardened (bulkhead; riprap) shorelines. Within 3 m from shore, the total fish/crustacean biomass was greatest at hardened shorelines, driven by greater water depth that facilitated access to planktivore (e.g., bay anchovy) and benthivore-piscivore (e.g., white perch) species. Small-bodied littoral-demersal species (e.g., Fundulus spp.) had greatest biomass at wetlands. By contrast, total biomass was comparable among shoreline types within 16 m from shore, suggesting the effect of shoreline hardening on fish biomass is largely within extreme nearshore areas immediately at the land/water interface. Shoreline type utilization was mediated by body size across all functional groups: small individuals (≤60 mm) were most abundant at wetlands and beaches, while large individuals (>100 mm) were most abundant at hardened shorelines. Taxonomic diversity analysis indicated natural shoreline types had more diverse assemblages, especially within 3 m from shore, although relationships with shoreline type were weak and sensitive to the inclusion/exclusion of crustaceans. Our study illustrates how shoreline hardening effects on fish/crustacean assemblages are mediated by functional group, body size, and distance from shore, with important applications for management.     

The abundance of estuarine larval and juvenile fish in a South Carolina intertidal creek

The fall and winter population of larval fish in a small intertidal creek was measured. The creek was blocked at high tide, and the immature fish were captured in a channel net designed for consistent quantitative sampling as they left with the ebbing tide. A total of 573,739 individuals with a biomass (preserved wet weight) of 66.1 kg were captured during the eight month sampling period (October 1974–May 1975). Twelve families, 13 genera, and 16 species were represented, with five species comprising 99.3% of the fish captured. The five species were:Leiostomus xanthurus (53.5%),Lagodon rhomboides (31.7%),Brevoortia tyrannus (11.9%),Micropogon undulatus (1.7%), andMyrophis punctatus (0.5%). The net was efficient, the catch was seasonal, and the greatest larval abundance occurred in February and March.     

Historical Comparison of Fish Community Structure in Lower Chesapeake Bay Seagrass Habitats

Seagrass beds provide important habitat for fishes and invertebrates in many regions around the world. Accordingly, changes in seagrass coverage may affect fish communities and/or populations, given that many species utilize these habitats during vulnerable early life history stages. In lower Chesapeake Bay, seagrass distribution has contracted appreciably over recent decades due to decreased water clarity and increased water temperature; however, effects of changing vegetated habitat on fish community structure have not been well documented. We compared fish community composition data collected at similar seagrass sites from 1976–1977 and 2009–2011 to investigate potential changes in species richness, community composition, and relative abundance within these habitats. While seagrass coverage at the specific study sites did not vary considerably between time periods, contemporary species richness was lower and multivariate analysis showed that assemblages differed between the two datasets. The majority of sampled species were common to both datasets but several species were exclusive to only one dataset. For some species, relative abundances were similar between the two datasets, while for others, there were notable differences without directional uniformity. Spot (Leiostomus xanthurus) and northern pipefish (Syngnathus fuscus) were considerably less abundant in the contemporary dataset, while dusky pipefish (Syngnathus floridae) was more abundant. Observed changes in community structure may be more attributable to higher overall bay water temperature in recent years and other anthropogenic influences than to changes in seagrass coverage at our study sites.     

Impact of common reed,<Emphasis Type="Italic">Phragmites australis</Emphasis>, on essential fish habitat: Influence on reproduction,embryological development,and larval abundance of mummichog (<Emphasis Type="Italic">Fundulus heteroclitus</Emphasis>)

The invasion ofSpartina marshes by the common reed,Phragmites australis, along the east coast of the United States over the last several decades has been well documented, although we know little about the impact of this invasion on the fish fauna and the few published papers seem contradictory. During 1999–2000 (May–September) we evaluated the fish response to vegetation type (Phragmites australis veersusSpartina alterniflora) by monitoring several aspects of fish early life history (egg deposition, embryonic development, hatching success, and larval and juvenile abundance) in low salinity marshes in the Mullica River in southern New Jersey. The dominant fish species using the marsh surface,Fundulus heteroclitus (93% of total catch, n=996 individuals), reproduced in both vegetation types with eggs deposited in leaf axils near the base of the plant inSpartina and in broken stems ofPhragmites during both years. These eggs also undergo successful embryonic development to hatching in both vegetation types. Larval and juvenile (5–75 mm total length, but 95% < 34 mm TL) abundance of this species is much reduced onPhragmites-dominated (mean CUPE=0.02, n=7 ind) marsh surface relative toSpartina (mean CPUE=2.31). These findings, and similar results for fish abundance in 1997 and 1998, indicate that theSpartima marsh surface is likely essential fish habitat for this species because it provides habitat for larvae and small juveniles, whilePhragmites does not. ThePhragmites invasion in brackish marshes may be having deleterious effects on fish populations and possibly on predators that prey uponF. heteroclitus, and as a result, marsh secondary production.     

Resident fishes and macrobenthos in mangrove-rimmed habitats: Evaluation of habitat restoration by hydrologic modification

An impounded area (Cabbagehead Bayou) in Upper Tampa Bay, Florida, was studied for 13 mo prior to and 22 mo after berm removal. Sampling for small fish and macrobenthos was conducted both at Cabbagehead Bayou and at a nearby control site, Double Branch Bay. Before and After Control and Impact (BACI) analyses, as well as similarity indices, were used to evaluate faunal characteristics in control versus impacted areas. Berm removal drastically changed periodicity of water cover in the impacted site, with the previously impounded site becoming almost entirely exposed during low tide. Fish abundances, biomass, and mean monthly number of species decreased in Cabbagehead Bayou after tidal flow was established as compared to when it was impounded. Responses of macrofauna varied among taxa, but total amphipod and polychaete abundance displayed a relative increase in the impacted site after berm removal. BACI analyses indicated that the relationship between mean values for almost all polychaete and amphipod taxa in the impacted and control sites changed significantly after berm removal. Additional differences were apparent in BACI analyses, which showed a significant change in the relationship of fish abundance and biomass at both sites for prebreach vs post-breach samples. The changes in relationships were generally not indicative of convergence of control and impacted sites, however. Community similarity of fish, amphipod, and polychaete assemblages increased during the last year of the post-breach sampling but remained generally very low. These findings suggest that distinct faunal responses to alteration of tidal periodicity can be detected within less than 2 yr after reestablishment of tidal flow. However, attainment of close correspondence to control conditions for certain fauna may require more than 22 mo. Therefore, future studies attempting to document recovery of restored wetlands may benefit from extended duration.     

Fish and invertebrate assemblages in seagrass, mangrove, saltmarsh, and nonvegetated habitats

Many studies compare utilization of different marine habitats by fish and decapod crustaceans; few compare multiple vegetated habitats, especially using the same sampling equipment. Fish and invertebrates in seagrass, mangrove, saltmarsh, and nonvegetated habitats were sampled during May–August (Austral winter) and December–January (Austral summer) in the Barker Inlet-Port River estuary, South Australia. Sampling was undertaken using pop nets in all habitats and seine nets in seagrass and nonvegetated areas. A total of 7,895 fish and invertebrates spanning 3 classes, 9 orders, and at least 23 families were collected. Only one fish species,Atherinosoma microstoma, was collected in all 4 habitats, 11 species were found in 3 habitats (mangroves, seagrass, and nonvegetated), and 13 species were only caught in seagrass and nonvegetated habitats. Seagrass generally supported the highest numbers of fish and invertebrates and had the greatest species richness. Saltmarsh was at the other extreme with 29 individuals caught from two species. Mangroves and nonvegetated habitats generally had more fish, invertebrates, and species than saltmarsh, but less than seagrass. Analyses of abundances of individual species generally showed an interaction between habitat and month indicating that the same patterns were not found through time in all habitats. All habitats supported distinct assemlages although seagrass and nonvegetated assemblages were similar in some months. The generality of these patterns requires further investigation at other estuaries. Loss of vegetated habitats, particularly seagrass, could result in loss of species richness and abundance, especially for organisms that were not found in other habitats. Although low abundances were found in saltmarsh and mangroves, species may use these habitats for varying reasons, such as spawning, and such use should not be ignored.     

Fish assemblages in the mangrove creeks of northern and southern Taiwan

A bimonthly study of the spatial variations in fish assemblages in the six mangrove creeks along the western coast of Taiwan was conducted from February 1996 to February 1997. Fyke nets were used to collect fishes in each of three creeks in the north (subtropical) and south (tropical) regions. A total of 79 fish species belonging to 33 families were collected and, of these, the Gobiidae, Mugilidae, Leiognathidae, and Cichlidae were the most diverse families. The fish assemblages in each creek were dominated by a small number of small fishes, most of which are the young of commercially important species. Their life cycles occurred to some extent in estuarine environments. Analyses by classification and ordination separated the assemblages into a northern group and a southern group and showed that the assemblages were far more temporally varied in the southern creeks than in the northern creeks. Fifty fish species were recorded in the northern creeks and 49 fish species in the southern creeks, with 20 species present in both regions. No significant difference in number of species per netting was detected between the regions. The number of individuals and biomass per netting were greater in the northern creeks than in the southern creeks. Rainfall and organic content of sediments may be responsible for the difference in fish abundance between the regions. In the northern creeks the assemblages were dominated by Liza macrolepis and Liza affinis in winter and spring, but the assemblages were more diverse in summer and fall. In the southern creeks, the assemblages were always characterized by several species and their dominance varied from month to month. The differences in the assemblage structure in northern and southern mangrove creeks are likely due to the oceanic current patterns around Taiwan.     

Spatial and temporal variation of the nekton and hyperbenthos from a temperate European estuary with regulated freshwater inflow

The aquatic macrofauna of the Guadalquivir estuary were sampled (1 mm mesh persiana net) at 5 sampling sites located along the entire (except the tidal freshwater region) estuarine gradient of salinity (outer 50 km). A total of 134 fish and macroinvertebrate species was collected but only 62 were considered common or regularly present in the estuary. Univariate measures of the community structure showed statistically significant differences among sampling sites: species richness, abundance, and biomass decreased in the upstream direction, being positively correlated with the salinity. Temporal differences of these three variables were also statistically significant. While a clear seasonal pattern (minimum densities in winter and maximum in spring-summer) was observed for abundance and biomass, no such pattern existed for the number of species. Mysids was the most dominant group throughout the estuary (96% to 99% of abundance; 49% to 85% of biomass), although fish biomass was also important at the outer estuary (36% to 38%). Multivariate analyses indicated highly significant spatial variation in the macrofaunal communities observed along the salinity gradient. These analyses suggest that the underlying structure was a continuum with more or less overlapping distributions of the species dependent on their ability to tolerate different physicochemical conditions. There were also significant temporal (intermonthly + interannual) variation of the estuarine community; the relative multivariate dispersion indicated that monthly variation was more considerable (relative multivariate dispersion >1) at the outer part of the estuary during the wet year (last 20 km) and was higher in the inner stations during the dry year (32 to 50 km from the river mouth). Since a clear negative exponential relationship was observed between the freshwater input (from a dam located 110 km upstream) and water salinity at all sampling stations, it is concluded that the human freshwater management is probably affecting the studied estuarine communities. While the higher seasonal (long-term) stability of the salinity gradient, due to the human control of the freshwater input, may facilitate the recruitment of marine species juveniles during the meteorologically unstable early-spring, the additional (short-term) salinity fluctuations during the warm period may negatively affect species that complete their lifecycle within the estuary.     

Littoral fish assemblages of the alien-dominated Sacramento-San Joaquin Delta,California, 1980–1983 and 2001–2003

We analyzed monthly boat electrofishing data to characterize the littoral fish assemblages of five regions of the Sacramento-San Joaquin Delta (northern, southern, eastern, western, and central), California, during two sampling periods, 1980–1983 (1980s) and 2001–2003 (2000s), to provide information pertinent to the restoration of fish populations in this highly altered estuary. During the 1980s, almost 11,000 fish were captured, including 13 native species and 24 alien species. During the 2000s, just over 39,000 fish were captured, including 15 native species and 24 alien species. Catch per unit effort (CPUE) of total fish, alien fish, and centrarchid fish were greater in the 2000s compared with the 1980s, largely because of increased centrarchid fish CPUE. These differences in CPUE were associated with the spread of submerged aquatic vegetation (SAV), particularly an alien aquatic macrophyte,Egeria densa. Native fish CPUE declined from the 1980s to the 2000s, but there was no single factor that could explain the decline. Native fish were most abundant in the northern region during both sampling periods. Nonmetric multidimensional scaling indicated similar patterns of fish assemblage composition during the two sampling periods, with the northern and western regions characterized by the presence of native species. The separation of the northern and western regions from the other regions was most distinct in the 2000s. Our results suggest that native fish restoration efforts will be most successful in the northern portion of the Delta. Management decisions on the Delta should include consideration of possible effects on SAV in littoral habitats and the associated fish assemblages and ecological processes.