A resource-based framework for establishing freshwater inflow requirements for the Suwannee River estuary

The availability of methods for establishing freshwater inflow requirements for estuaries lags behind those for establishing flow requirements in riverine ecosystems. Some of the basic principles and approaches for establishing riverine flow requirements may be applicable to estuaries. An emerging approach for establishing freshwater inflow needs for the Suwannee River estuary involves maintaining a natural inflow regime (in terms of magnitude, frequency, duration, and timing of freshwater flows) and identifying important habitat targets to be protected. The salinity-river flow conditions needed to sustain the habitat targets in their existing condition are then identified. A variety of tools are employed, such as salinity metrics, biological metrics, limits of distribution of communities or habitats, and landscape-scale characteristics to define the salinity and corresponding flow ranges needed to protect and maintain the resource targets. With this information, combined with use of models to evaluate flow-salinity relationships and various withdrawal scenarios, river flow criteria can be set which address the freshwater inflow requirements to maintain these ranges. Subsequentmonitoring and research is undertaken to evaluate the effectiveness of the river flow criteria in protecting the estuarine resource targets. This information can be used to subsequently confirm, refine, or modity the flow criteria.     

A method to assess the freshwater inflow requirements of estuaries and application to the Mtata estuary, South Africa

The National Water Act (Act 36 of 1998) in South Africa recognizes basic human water requirements as well as the need to sustain the country's freshwater and estuarine ecosystems in a healthy condition for present as well as future generations. In this Act, provision is made for a water reserve to be estimated prior to the authorization of water use (e.g., for agriculture, large volume residential and industrial uses) through licensing. This reserve is the water required to satisfy basic human needs (i.e., 25 1 person^?1 d^?1) and to protect aquatic ecosystems to ensure present and future sustainable use of the resource. This led the Departments of Water Affairs and Forestry and estuarine scientists throughout South Africa to develop a method to determine the freshwater inflow requirements of estuaries. The method includes documenting the geographical boundaries of the estuary and determining estuarine health by comparing the present state of the estuary with a predicted reference condition with the use of an Estuarine Health Index. The importance of the estuary as an ecosystem is taken from a national rating system and together with the present health is used to set an Ecological Reserve Category for the estuary. This category represents the level of protections afforded to an estuary. Freshwater is then reserved to maintain the estuary in that Ecological Reserve Category. The Reserve, the quantity and quality of freshwater required for the estuary, is determined using an approach where realistic future river runoff scenarios are assessed, together with data for present state and reference conditions, to evaluate the extent to which abiotic and biotic conditions within an estuary are likely to vary with changes in river inflow. Results from these evaluations are used to select an acceptable river flow scenario that represents the highest reduction in freshwater inflow that will still protect the aquatic ecosystem of the estuary and keep it in the desired Ecological Reserve Category. The application of the Reserve methodology to the Mtata estuary is described.     

A conceptual model of estuarine freshwater inflow management

As humans continue to influence the quantity, timing, and quality of freshwater input to estuaries, it is becoming increasingly common for policies to be enacted that mandate the establishment of freshwater inflow criteria that will serve to preserve and protect estuarine ecosystems. This paper reviews the scientific literature describing how changes in freshwater inflow affect estuaries, proposes a conceptual model that explores the roles of scientists, citizens, politicians, and managers in the management of freshwater inflow to estuaries, and uses the model to explore the ways in which freshwater inflow is managed in a variety of estuaries. The scientific review is organized to provide an overview of the connections between freshwater inflow (in terms of the quantity, quality, and timing of water delivery), estuarine conditions (such as salinity and concentrations of dissolved and particulate material), and estuarine resources (such as the distribution and abundance of organisms), and to highlight our understanding of the causative mechanisms that underlie the relationships among these variables. The premise of the conceptual model is that the goal of estuarine freshwater inflow policy is to protect those resources and functions that we as a society value in estuaries, and that management measures use scientific information about the relationships among inflow, conditions, and resources to establish inflow standards that can meet this goal. The management approach can be inflow-based (flow is kept within some prescribed bounds under the assumption that taking too much away is bad for the resources), condition-based (inflow standards are set in order to maintain specified conditions in the estuary), or resource-based (inflow standards are set based on the requirements of specific resources), but each of these is carried out by regulating inflow. This model is used as a framework to describe the development of freshwater inflow criteria for estuaries in Texas, Florida, and California.     

The effect of freshwater inflow on meiofaunal and macrofaunal populations in the Guadalupe and Nueces Estuaries,Texas

Two estuaries with very different inflow characteristics were compared to test the hypothesis that benthic standing crops are enhanced by freshwater inflow. Assuming predation pressure is similar in both estuaries, this would imply that freshwater inflow enhances secondary production. The Guadalupe Estuary had 79 times more freshwater inflow than the Nueces Estuary, and a third of the salinity. The Guadalupe had higher macrofaunal densities and biomass than the Nueces, and both parameters increased with decreasing salinity within the Guadalupe Estuary. Macrofauna density increased with increasing salinity in the Nueces Estuary, due to invasion by marine species. However, meiofauna population size responds differently than macrofauna. Meiofaunal densities were higher in the low-inflow Nueces Estuary, and increased with increasing salinity in both estuaries. Macrofauna diversity increased with salinity, both within and between estuaries. The macrofauna response supports the hypothesis that increased freshwater inflow stimulates secondary production. A review of past benthic studies in these estuaries and the historical climatic patterns indicate that wet years with high inflow result in increased macrofaunal productivity. Since, macrofaunal diversity decreased with lower salinity both within and between the estuaries, the enhanced productivity is due to increases by freshwater and estuarine species that can tolerate low salinities. Increased macrofaunal densities are associated with decreasing meiofaunal densities. The latter result could be due to either increased macrofaunal competition with or predation on meiofauna, or a lack of low-salinity tolerance by meiofauna.     

河口生态需水研究进展

针对陆海交互作用下河口生态需水影响因素多且时空差异性显著的特点,在系统分析淡水输入对河口生态系统水环境过程和生物过程影响的基础上,按生态需水目标的差异,将河口生态需水分析方法划分为基于典型生物资源保护目标、基于生境保护目标以及基于多目标整合分析3种类型。从生态需水目标筛选、生态需水目标对淡水输入响应关系以及生态需水计算方法实用性方面探讨了河口生态需水研究中面临的主要问题。结论认为生态系统健康综合表征指标的确定应成为分析河口生态需水的关键科学基础,筛选控制性生态要素构建河口关键生态水文过程模型可成为有效提高生态需水计算方法实用性的主要技术手段。     

Use of a particle-tracking model for predicting entrainment at power plants on the Hudson River

A major assumption of the Empirical Transport Model (ETM), widely adopted by both electric utilities and regulatory agencies for estimating the effects of entrainment mortality on fish populations in estuaries, is that the fraction of ichthyoplankton entrained varies only in response to changes in water withdrawals, not to changes in freshwater flow. We evaluated this assumption using a particle-tracking model to estimmate the probability of entrainment at power plants on the Hudson River during low and high freshwater flow periods and comparing those probabilities with estimates calculated from the ETM. We found that freshwater flow had a profound effect on the probability of entrainment. Both the number of river regions from which particles were entrained and the probabilities of entrainment for particles in those river regions differed between low-flow and high-flow periods. During high flow, particles spent less time in the grid box next to the intakes, reducing the probability of entrainment for particles released in the river region of each power plant and the average probability of entrainment across all regions at three power plants. The reduced probability of entrainment for particles released in the river regions of two power plants was offset by higher entrainment for particles upriver of these power plants. Although the average probabilities of entrainment across all river regions estimated with the particle-tracking model and the ETM were relatively similar for some power plants at high flow, low flow, or both, the probabilities for each river region differed considerably between the models. The number of river regions from which particles were entrained using the ETM was consistently undersestimated, resulting in probabilities for regions where entrainment occurred that were biased high compared with the particle-tracking model.     

Mainstem and Backwater Fish Assemblages in the Tidal Caloosahatchee River: Implications for Freshwater Inflow Studies

Research strategies for investigating the freshwater-inflow requirements of estuarine fishes often integrate life-history information and correlative analyses of inflow and fish abundance. In tidal rivers, however, some fish have affinities for embayments, oxbows, and smaller tributaries, often referred to collectively as river “backwaters”. The objective of this study was to determine whether freshwater and estuarine fish assemblages differed between backwaters and the mainstem of the tidal Caloosahatchee River, a highly managed river system located in an urban setting in southwest Florida. Nonmetric multidimensional scaling of 21.3-m seine data revealed that fish assemblages did indeed differ between the backwater and mainstem habitats in each of three river sections. Univariate analyses identified species that differed in abundance between the habitats, which included ecologically and economically important fishes in the region. For example, striped mullet Mugil cephalus and pinfish Lagodon rhomboides were more abundant along the river's mainstem; common snook Centropomus undecimalis and bluegill Lepomis macrochirus were more abundant in the river's backwaters. For those species that were more abundant along the mainstem of the river or showed no difference, studies that measure changes in the distribution and abundance of these species with varying inflow along the mainstem of the river are justified. However, for species that were more abundant in backwater areas, geomorphological features should be considered in the design of studies that assess factors affecting fish use.     

Impact assessment of Three Gorges Dam’s impoundment on river dynamics in the north branch of Yangtze River estuary,China

As one of the world’s largest hydropower projects, the Three Gorges Dam (TGD)’s 156–175 m height storing test in flood recession seasons during 2006–2011 has aroused international attention. The novel approaches of cross-wavelet transform and wavelet coherence were firstly introduced to reveal the significant coherence and time lag property in time–frequency space between river dynamics in hydrological stations along Yangtze River. Then, using the optimum lag time nodes, corresponding regression models between river dynamics in these stations were established and utilized to assess the river dynamics in stations downstream under the impact of TGD’s impoundment. Results showed that the average decrease ratio of 24.3 % in the Three-Gorge reservoir outflow was caused in TGD’s impounding periods during 2006–2011. The corresponding average decrease ratios of 25.1, 16.5 and 1.9 % in Yichang flow, Datong flow (with 6 days lag), and estuarine Santiao river stage (with 32 days lag), respectively, were caused by TGD’s impoundment during 2006–2011. In addition, the impact weights of multiple driving factors on estuarine river dynamics were discussed, and the main factor of the combined impacts of estuarine tidal fluctuation and sea level change while the secondary factor of the upper stream inflow were demonstrated. A further suggestion about the optimization design of TGD’s safety impounding scheme was proposed to prevent estuarine saline water intrusion by guaranteeing the average daily increase of Three Gorges reservoir water level lower than 1.11 m/day during TGD’s impounding period.     

Physical, biological, and management responses to variable freshwater flow into the San Francisco Estuary

Freshwater flow is the principal cause of physical variability in estuaries and a focus of conflict in estuaries where a substantial fraction of the freshwater is diverted. Variation in freshwater flow can have many effects: inundation of flood plains, increase loading and advective transport of materials and organisms, dilution or mobilization of contaminants, compression of the estuarine salinity field and density gradient, increase in stratification, and decrease in residence time for water while increasing it for some particles and biota. In the San Francisco Estuary, freshwater flow is highly variable, and has been altered by shifts in seasonal patterns of river flow and increases in diversions from tidal and nontidal regions, entraining fish of several species of concern. Abundance or survival of several estuarine-dependent species also increases with freshwater outflow. These relationships to flow may be due to several potential mechanisms, each with its own locus and period of effectiveness, but no mechanism has been conclusively shown to underlie the flow relationship of any species. Several flow-based management actions were established in the mid-1990s, including a salinity standard based on these flow effects, as well as reductions in diversion pumping during critical periods for listed species of fish. The effectiveness of these actions has not been established. To make the salinity standard more effective and more applicable to future estuarine conditions will require investigation to determine the underlying mechanisms. Effects of entrainment at diversion facilities are more straightforward conceptually but difficult to quatify, and resolving these may require experimental manipulations of diversion flow.     

Seasonal changes in the nekton community of the Suwannee River estuary and the potential impacts of freshwater withdrawal

In Florida, issues related to alterations of estuarine salinity caused by freshwater withdrawal have recently gained increasing attention. We examined nekton community structure in the Suwannee River estuary (1997–2000) and investigated the relationship between environmental factors and the abundance of fisheries resources. We compared nekton community structure and environmental factors seasonally and annually using multidimensional scaling (MDS) ordination and cluster analysis and observed a strong seasonal pattern. This pattern was consistent among years and closely paralleled those for temperature and river discharge. Representative species for cold seasons includedLeiostomus xanthurus andLagodon rhomboides, and those for warm seasons includedMembras martinica andAnchoa hepsetus. Species that contributed most to the dissimilarity in community structures between wet and dry seasons were abundant and generally preferred lower salinity (e.g.,L. xanthurus, Eucinostomus spp., andMenidia spp.). A period of low freshwater inflow during the latter portion of our study coincided with both decreases and increases in the abundances of some dominant and some economically important species. We have established a baseline which will assist in measuring the effects of long-term changes in freshwater input on the nekton communities of the Suwannee River estuary, but our ability to predict these effects is still limited.     

Nutrient biogeochemistry in an upwelling-influenced estuary of the Pacific northwest (Tillamook Bay,Oregon, USA)

Tillamook Bay, Oregon, is a drowned river estuary that receives freshwater input from 5 rivers and exchanges ocean water through a single channel. Similar to other western United States estuaries, the bay exhibits a strong seasonal change in river discharge in which there is a pronounced winter maximum and summer minimum in precipitation and runoff. The behavior of major inorganic nutrients (phosphorus, nitrogen, and silica) within the watershed is examined over seasonal cycles and under a range of river discharge conditions for October 1997–December 1999. Monthly and seasonal sampling stations include transects extending from the mouth of each river to the mouth of the estuary as well as 6–10 sites upstream along each of the 5 major rivers. Few studies have examined nutrient cycling in Pacific Northwest estuaries. This study evaluates the distributions of inorganic nutrients to understand the net processes occurring within this estuary. Based upon this approach, we hypothesize that nutrient behavior in the Tillamook Bay estuary can be explained by two dominant factors: freshwater flushing time and biological uptake and regeneration. Superimposed on these two processes is seasonal variability in nutrient concentrations of coastal waters via upwelling. Freshwater flushing time determines the amount of time for the uptake of nutrients by phytoplankton, for exchange with suspended particles, and for interaction with the sediments. Seasonal coastal upwelling controls the timing and extent of oceanic delivery of nutrients to the estuary. We suggest that benthic regeneration of nutrients is also an important process within the estuary occurring seasonally according to the flushing characteristics of the estuary. Silicic acid, nitrate, and NH₄ ⁺ supply to the bay appears to be dominated by riverine input. PO₄ ⁻³ supply is dominated by river input during periods of high river flow (winter months) with oceanic input via upwelling and tidal exchange important during other times (spring, summer, and fall months). Departures from conservative mixing indicate that internal estuarine sources of dissolved inorganic phosphorus and nitrogen are also significant over an annual cycle.     

Positive Relationship between Freshwater Inflow and Oyster Abundance in Galveston Bay,Texas

Analysis of fisheries-independent data for Galveston Bay, Texas, USA, since 1985 shows eastern oysters (Crassostrea virginica) frequently demonstrate increased abundance of market-sized oysters 1 to 2 years after years with increased freshwater inflow and decreased salinity. These analyses are compared to Turner’s (Estuaries and Coasts 29:345–352, 2006) study using 3-year running averages of oyster commercial harvest since 1950 in Galveston Bay. Turner’s results indicated an inverse relationship between freshwater inflow and commercial harvest with low harvest during years of high inflow and increased harvest during low flow years. Oyster populations may experience mass mortalities during extended periods of high inflow when low salinities are sustained. Conversely, oyster populations may be decimated during prolonged episodes of low flow when conditions favor oyster predators, parasites, and diseases with higher salinity optima. Turner’s (Estuaries and Coasts 29:345–352, 2006) analysis was motivated by a proposed project in a basin with abundant freshwater where the goal of the project was to substantially increase freshwater flow to the estuary in order to increase oyster harvest. We have the opposite concern that oysters will be harmed by projects that reduce flow, increase salinity, and increase the duration of higher salinity periods in a basin with increasing demand for limited freshwater. Turner’s study and our analysis reflect different aspects of the complex, important relationships between freshwater inflow, salinity, and oysters.     

Manganese and suspended matter in the Yaquina Estuary,Oregon

The longitudinal distribution of total suspended matter and total, dissolved, and particulate manganese in a small coastal plain estuary is described. The distribution of manganese is a consequence of estuarine circulation; a within-estuary maximum is inversely correlated with river flow, and is a function of residence time in the estuary, resuspension in the upper estuary, and desorption from particles introduced from within the estuary or from the river. The turbidity maximum is similarly most pronounced during low river flows. The upper estuary (salinity <15‰), comprising a small percentage of the total estuary volume during low flow, receives material from the river and along the bottom from the lower estuary; this material is returned to the water column by resuspension and desorption from estuarine and riverine particles. The lower estuary tends to damp out these processes because of the greater volume and (residence) time available for mixing.     

Effect of irrigation pumpage during drought on karst aquifer systems in highly agricultural watersheds: example of the Apalachicola-Chattahoochee-Flint river basin,southeastern USA

In the Apalachicola-Chattahoochee-Flint (ACF) river basin in Alabama, Georgia, and Florida (USA), population growth in the city of Atlanta and increased groundwater withdrawal for irrigation in southwest Georgia are greatly affecting the supply of freshwater to downstream regions. This study was conducted to understand and quantify the effect of irrigation pumpage on the karst Upper Floridan Aquifer and river–aquifer interactions in the lower ACF river basin in southwest Georgia. The groundwater MODular Finite-Element model (MODFE) was used for this study. The effect of two drought years, a moderate and a severe drought year, were simulated. Comparison of the results of the irrigated and non-irrigated scenarios showed that groundwater discharge to streams is a major outflow from the aquifer, and irrigation can cause as much as 10 % change in river–aquifer flux. The results also show that during months with high irrigation (e.g., June 2011), storage loss (34 %), the recharge and discharge from the upper semi-confining unit (30 %), and the river–aquifer flux (31 %) are the major water components contributing towards the impact of irrigation pumpage in the study area. A similar scenario plays out in many river basins throughout the world, especially in basins in which underlying karst aquifers are directly connected to a nearby stream. The study suggests that improved groundwater withdrawal strategies using climate forecasts needs to be developed in such a way that excessive withdrawals during droughts can be reduced to protect streams and river flows.     

Food Web Structure and Habitat Connectivity in Fish Estuarine Nurseries—Impact of River Flow

River flow variability is known to influence estuarine production, yet knowledge on its effect upon estuarine food webs dynamics is still scarce. Stable carbon and nitrogen isotopes were used to assess the effect of river flow in the connectivity and food web interactions between the two main fish nursery areas of the Tagus estuary. The aims of the present work were to investigate the seasonal variation in food web structure and the exchange rate of individuals of marine juvenile fish among estuarine nurseries, to compare the spring of a rainy year (2001) with that of an average year (2000), and to investigate the impact of the winter floods of 2001. A low level of connectivity was observed for the fish species that use these areas as nurseries. In low river flow conditions, two isotopically distinct food webs were established in each nursery area. These food webs were very sensitive to small variations in the freshwater input. Winter floods seem to disrupt the localized food webs that are established in low river flow periods, leading to the re-establishment of a wider food web. While in rainy years this wide food web is maintained until spring, in average years the food web undergoes fragmentation into two localized and isotopically distinctive food webs. The increase in frequency of droughts due to climate change should lower the connectivity of the estuarine fish nurseries food webs, causing habitat fragmentation and consequent loss in complexity and resilience.     

Downstream effects of water withdrawal in a small,high-gradient basin: Erosion and deposition on the Skokomish River delta

The purpose of this paper is to analyze downstream effects of freshwater flow diversion from a small, active-continental-margin river basin. The Skokomish River delta is a tributary estuary to Hood Canal in Washington state that receives drainage from the southeastern side of the Olympic Mountains. Its drainage basin is steep, and rainfall is high. Approximately 40% of the annual average runoff of the entire system has been diverted from the North Fork Skokomish River for power production since completion of two dams in 1930; this water does not pass through the lower river or over the delta. Extensive logging has occurred in the remainder of the basin. Comparison of prediversion (1885) and postdiversion (1972) bathymetric surveys shows that deposition (about 0.013 to 0.022 m yr^?1) has occurred on the inner delta and erosion (up to 0.033 m yr^?1) on the outer delta. This steepening of the delta surface has apparently been caused by a loss of sediment transport capacity in the lower river and estuary combined with an increased sediment supply due to logging. Although the total area of unvegetated tidal flats thas decreased by only about 6%, there has been a more than 40% loss of highly productive low intertidal surface area. A conservative estimate of loss of eelgrass (Zostera marina) beds is 18%; a reduction in the size of mesohaline mixing zone has also occurred. These habitat losses are similar to those observed elsewhere in the world in larger river basins that have suffered water withdrawals of the same magnitude, but their impacts cannot either be evaluated or understood causally through consideration of simple measures like changes total estuarine deltaic area. Evaluation of estuarine effects of anthropogenic modification must, therefore, include consideration of both changes in habitat function and in the physical processes. These must be evaluated within the totality of the river basin-estuary system that cause these changes. In this case, sediment transport constitutes the critical link between fluvial alterations and the remote downstream, estuarine consequences thereof.     

Is the Response of Estuarine Nekton to Freshwater Flow in the San Francisco Estuary Explained by Variation in Habitat Volume?

Abundance of estuarine biota can vary with freshwater inflow through several mechanisms. One proposed mechanism is that the extent of physical habitat for an estuarine species increases with flow. We estimated the contribution of variation in habitat volume to the responses of eight species of estuarine nekton to changes in freshwater flow in the San Francisco Estuary. Resource selection functions for salinity and depth were developed for each species (and for five additional species) using five monitoring data sets. The TRIM3D hydrodynamic model was run for five steady flow scenarios to determine volume by salinity and depth, and resource selection functions were used as a weighting factor to calculate an index of total habitat for each species at each flow. The slopes of these habitat indices vs. flow were consistent with slopes of abundance vs. flow for only two of the species examined. Therefore, other mechanisms must underlie responses of abundance to flow for most species.     

Chesapeake Bay Plume Morphology and the Effects on Nutrient Dynamics and Primary Productivity in the Coastal Zone

To determine the effects of the Chesapeake Bay outflow plume on the coastal ocean, nutrient concentrations and climatology were evaluated in conjunction with nitrogen (N) and carbon (C) uptake rates during a 3-year field study. Sixteen cruises included all seasons and captured high- and low-flow freshwater input scenarios. Event-scale disturbances in freshwater flow and wind speed and direction strongly influenced the location and type of plume present and thus the biological uptake of N and C. As expected, volumetric primary productivity rates did not always correlate with chlorophyll a concentrations, suggesting that high freshwater flow does not translate into high productivity in the coastal zone; rather, high productivity was observed during periods where recycling processes may have dominated. Results suggest that timing of meteorological events, with respect to upwelling or downwelling favorable conditions, plays a crucial role in determining the impact of the estuarine plume on the coastal ocean.     

Estimation of net physical transport and hydraulic residence times for a coastal plain estuary using box models

A box model based on salinity distributions and freshwater inflow measurements was developed and used to estimate net non-tidal physical circulation and hydraulic residence times for Patuxent River estuary, Maryland, a tributary estuary of Chesapeake Bay. The box model relaxes the usual assumption that salinity is at steady-state, an important improvement over previous box model studies, yet it remains simple enough to have broad appeal. Average monthly 2-dimensional net non-tidal circulation and residence times for 1986–1995 are estimated and related to river flow and salt water inflow as estimated by the box model. An important result is that advective exchange at the estuary mouth was not correlated with Patuxent River flow, most likely due to effects of offshore salinity changes in Chesapeake Bay. The median residence time for freshwater entering at the head of the estuary was 68 d and decreased hyperbolically with increasing river flow to 30 d during high flow. Estimates of residence times for down-estuary points of origin showed that, from the head of the estuary to its mouth, control of flushing changed from primarily river flow to other factors regulating the intensity of gravitational circulation.     

Effects of the 2004 hurricanes on the fish assemblages in two proximate southwest Florida estuaries: Change in the context of interannual variability

We examined interannual differences in fish assemblage structure in Tampa Bay and Charlotte Harbor, Florida, from 1996 to 2005 to reveal the extent of hurricane-induced changes in relation to multiannual variability for five different assemblages in each estuary: small-bodied fishes (<generally 80-mm standard length) along river shorelines, in river channels, along bay shorelines, and on the bay shelf (<1.5-m water depth); and large-bodied fishes (>generally 100-mm standard length) along bay shorelines. Fish assemblages tended to differ, between estuaries, as did interannual variability in assemblage structure. In the lower portions of tributary rivers to Tampa Bay, the small-bodied shoreline fish assemblage during August 2004 to July 2005, i.e., during and after the multiple hurricanes, was different from assemblages of August to July in previous years. This may have been a result of physical displacement of fish or suboptimal salinities caused by increased freshwater inflow. The small-bodied shoreline fish assemblage in Charlotte Harbor also differed between prehurricane and hurricane periods, possibly because damage to vegetated shorelines affected fish survival through a decrease in feeding and refuge habitats. In the remaining habitats, fish assemblage structure from August 2004 to July 2005 were within the range of variability exhibited over the 9-yr study period. There were several unusual fish assemblages that appeared to be attributable to drought conditions (1996, 1999–2000), suggesting that other major environmental perturbations may be as important as hurricanes in influencing assemblage structure. We conclude that although the 2004 hurricane season affected some of the fish assemblages of Tampa Bay and charlotte Harbor, these assemblages generally appeared quite resilient to natural environmental perturbations from a decadal perspective.