Alan K. Whitfield, Emeritus Chief Scientist, South African Institute for Aquatic Biodiversity (SAIAB), Grahamstown, Eastern Cape Province, South AfricaKenneth W. Able, Professor Emeritus, Marine Field Station, Rutgers University, Tuckerton, New Jersey, USA Stephen J. M. Blaber, Honorary Fellow, CSIRO Marine Research, Brisbane, Queensland, Australia Michael Elliott, Director, International Estuarine & Coastal Specialists Ltd, Leven, UK and Professor in Estuarine & Coastal Sciences, University of Hull, Hull, UK

• DedicationPrefaceAuthor DetailsAcknowledgementsChapter 1: Introduction1.1 Scope of the book1.2 Reasons why this synthesis is important1.3 Estuary definition and types1.4 Chapter descriptions1.5 Conclusions1.6 ReferencesChapter 2: Fish Assemblages and Functional Groups 2.1 Introduction2.2 Zoogeography and estuarine fish assemblages2.3 Estuarine typology and fish assemblages2.4 Fish guilds and functional groups2.4.1 Estuarine Use Functional Group (EUFG)2.4.2 Feeding Mode Functional Group (FMFG)2.4.3 Reproductive Mode Functional Group (RMFG)2.5 Do functional groups drive fish assemblage structure?2.6 Fish functional groups and guild analyses2.7 Acknowledgements2.8 ReferencesChapter 3: Reproduction, Ontogeny and Recruitment 3.1 IntroductionScope of the Chapter3.2 Estuarine support of reproduction and recruitment3.2.1 Replenishment: modes and patterns3.2.1.1 Modes of reproduction3.2.1.2 Early life stages and nurseries3.2.2 Sources of variability in reproductive success and recruitment3.2.2.1 Habitat and water quality3.2.2.2 Hydrography and physics3.2.2.3 Foods of early life stages3.2.2.4 Predators3.2.2.5 Weather, climate and estuarine change3.3 Early-life stages and recruitment dynamics3.3.1 Dispersal, transport and retention3.3.1.1 Offshore to estuary transport processes3.3.1.2 Swimming as a transport mechanism3.3.1.3 Near- and within-estuary transport processes3.3.1.4 Retention: estuarine features and processes3.3.2 Settlement3.3.3 Larval and juvenile production processes3.3.3.1 Larval feedingOntogenetic shifts and feeding successNutritional considerations3.3.4 Larval and juvenile production: growth and mortality3.3.4.1 Rates and variabilityStage durations3.3.4.2 Predation3.3.4.3 Environmental factors3.4 Adults and recruitment3.4.1 Adult stock3.4.1.1 Stock structure, contingents and cohorts3.4.1.2 Maternal effects3.4.2 Scales and patterns of variability in reproductive success3.4.2.1 Recruitment levels and variability3.4.2.2 Adult stock and recruitment3.4.2.3 Predicting and forecasting recruitment3.4.3 Recruitment: an integrated, evolved process3.5 Threats to reproduction and recruitment in estuaries3.5.1 Excessive fishing: depletion of adults and bycatch of juveniles3.5.2 Habitat destruction and degradation3.5.3 Impoundments and flow regulation3.5.4 Power plants3.5.5 Estuary contaminants, water quality degradation3.5.6 Eutrophication3.5.7 Climate change3.5.8 Catastrophic events3.6 Case Studies3.6.1 Pleuronectiformes3.6.2 Sciaenidae3.6.3 Anchoa mitchilli (Engraulidae)3.6.4 Brevoortia tyrannus and Brevoortia spp. (Clupeidae)3.6.5 Morone saxatilis (Moronidae)3.6.6 Gadidae and Clupeidae (Baltic Sea)3.6.7 Lateolabrax japonicus (Lateolabracidae)3.6.8 Fundulus heteroclitus (Fundulidae)3.7 Summary and conclusions3.8 Acknowledgements3.9 ReferencesChapter 4: Habitat Use and Connectivity4.1 Introduction4.2 Habitat diversity4.2.1 Water column habitat4.2.2 Unstructured shallow habitats4.2.3 Structured benthic habitats4.2.3.1 Salt marshes4.2.3.2 Submerged aquatic vegetation4.2.3.3 Mangroves4.2.3.4 Shellfish beds4.2.3.5 Woody debris4.2.3.6 Rocky and gravel bottoms4.3 Geomorphological and hydrological variables4.4. Physico-chemical variables4.5 Dynamics of juvenile habitat use4.5.1 Temperature effects4.5.2 Salinity effects4.5.3 Diadromy4.5.4 Settlement habitats4.5.5 Connectivity among habitats4.5.6 Alien species4.6 Adult habitat4.7 Habitat fidelity and juvenile and adult fishes4.8 Ecological context4.9 Connectivity between estuarine, freshwater and marine ecosystems4.9.1 Migrations into estuaries4.9.2 Migrations out of estuaries4.9.3 Migrations between estuaries4.10 Conclusions4.11 Acknowledgements4.12 References*Chapter 5: Feeding Ecology and Trophic Dynamics5.1 Introduction5.2 Fish foraging behaviour and food intake5.2.1 Prey detection5.2.2 Feeding periodicity5.2.3 Food intake5.2.4 Feeding movements and migrations5.3 Factors influencing feeding ecology5.3.1 Environmental factors5.3.1.1 Water temperature, salinity and dissolved oxygen5.3.1.2 Tidal regime and substratum composition5.3.2 Biological factors5.3.2.1 Body size5.3.2.2 Ontogenetic changes in fish diets5.3.3 Foraging specializations5.3.4 Opportunistic versus specialised feeding5.4 Ecotrophomorphology5.5 Trophic categorization5.5.1 Herbivorous species5.5.2 Detritivorous species5.5.3 Zoobenthivorous species5.5.4 Zooplanktivorous species5.5.5 Piscivorous species5.5.5.1 Cannabilism5.6 Competition, resource partitioning, energy flow and connectivity5.6.1 Intraspecific and interspecific competition5.6.2 Resource portioning5.6.3 Energy flow and connectivity5.7 Fishbase approach to Functional Feeding Groups5.7.1 Example of a FFG analysis5.8 Fish food sources in estuaries5.8.1 Submerged macrophyte habitats5.8.2 Emergent macrophyte habitats5.9 Food web complexity5.9.1 Vertical and horizontal feeding patterns by fishes5.10 Predators of fish in estuaries5.10.1 Invertebrates5.10.2 Birds5.10.3 Reptiles5.10.4 Mammals5.11 Effects of natural and anthropogenic perturbations on food webs5.12 Acknowledgements5.13 ReferencesChapter 6: Fishes and Estuarine Environmental Health6.1 Estuarine environmental health: concepts, definitions and assessment6.2 Anthropogenic pressures impacting estuarine fish assemblages6.2.1 Habitat loss and physical degradation6.2.2 Pollution6.2.3 River flow regulation6.2.4 Fisheries and aquaculture6.2.5 Non-indigenous species6.2.6 Climate change6.2.7 Integration of human pressures: the global change context6.3 Fishes biomarkers responding to human pressures6.3.1 Fish biomarkers and biomagnification6.3.2 Biomarkers of exposure6.4 Fishes as biological indicators6.5 Main methodological approaches to assess estuarine health using fish as indicators6.5.1 Historical data and reference conditions6.5.2 Experimental approaches6.5.3 Environmental impact assessment and other risk assessment methods6.5.4 Qualitative methods6.5.5 Quantitative indicators6.5.6 Models6.6 Environmental health fish-based indices6.7 Disentangling fish responses in the multi-stress context of global changes6.7.1 Univariate approaches6.7.2 Multivariate approaches6.8 Future research directions6.9 ReferencesChapter 7: Climate Change and Fishes in Estuaries7.1 Introduction7.2 Global, regional and local patterns7.2.1 Predictors of fish taxonomic diversity at global and regional scales7.2.2 Predictors of fish taxonomic diversity at local scales7.2.3 Predictors of fish functional diversity at global, regional and local scales7.3 Potential impacts of environmental/climate stressors on estuarine fish7.3.1 Salinity and freshwater flow impacts7.3.2 Temperature impacts7.3.3 Dissolved oxygen impacts7.3.4 Impacts of elevated CO27.3.5 Sea level rise7.3.6 Estuary entrance channel openings and fish access7.3.7 Disease7.4 Climate change and fisheries in estuaries7.4.1 Links to fisheries catches7.4.2 Socio-economic effects and management implications7.5 Case studies7.5.1 Arctic7.5.2 Temperate northern Atlantic7.5.3 Temperate northern Pacific7.5.4 Tropical Atlantic7.5.5 Indo-Pacific7.5.6 Temperate South America7.5.7 Temperate southern Africa7.5.8 Temperate Australia7.6 Gaps in knowledge and future research directions7.7 Acknowledgements7.8 ReferencesChapter 8: Estuarine Degradation and Rehabilitation8.1 Introduction8.1.1 Hazards and risks to estuarine fish and fisheries and their habitats8.1.2 Effects of climate change on estuarine fish and fisheries8.1.3 Effects of estuarine degradation on ecosystem services8.1.4 Effects of estuarine degradation on water quality and impacts on fish8.1.5 Heavy metals8.1.6 Organic pollutants8.1.7 Pharmaceutical and personal care products8.1.8 Nutrients8.1.9 Effects on water quantity, hydropeak and flow alteration on fish8.1.10 Effects on fishing8.2 Estuarine restoration and habitat creation8.3 Current practices8.4 Ecological engineering8.5 Contribution of modelling tools to more process-based restoration objectives8.5.1 Introduction8..5.2 Framework8.5.2.1 Towards a more process-orientated approach8.5.2.2 Towards integrated objectives8.6 Why modelling processes?8.6.1 Physical phenomena8.6.2 Species use of the estuarine environment and compartmental interactions8.6.3 Overview8.7 Modelling tools8.7.1 Biogeochemical modelling8.7.2 Hydromorphological-sedimentary modelling8.8 Life cycle modelling8.8.1 ‘Static’ approaches: statistical habitat suitability8.8.2 Dynamic approach: the probability to attaining suitable habitats8.9 Food web modelling8.10 The way forward8.11 From theory to practice8.11.1 A case study of restoration in the Schelde Estuary8.11.2 Ecological restoration by opportunity: an example from the Gironde Estuary8.11.2.1 Gironde restoration summary8.11.3 Case study – restoration of former salt hay farms8.11.4 Case study – habitat alteration and restoration linked to a common reed invasion8.11.5 Restoration of whole estuaries and wetland systems8.12 Concluding comments8.13 Acknowledgements8.14 ReferencesChapter 9: Estuarine Fisheries9.1 Introduction9.2 Estuarine fishery sectors9.3 Problems and issues in fisheries9.4 Fishery yields9.5 Estuarine fisheries: a selection of case studies9.5.1 Asian fisheries9.5.1.1 The Hilsa Fishery, South Asia9.5.1.2 The Lake Chilika Fishery, India9.5.1.3 The Pichavaram Fishery, India9.5.1.4 The Larut-Matang Fishery, Indonesia9.5.2 African fisheries9.5.2.1 The Kosi Bay Lakes Fishery, South Africa9.5.2.2 The Sundays Estuary Fishery, South Africa9.5.2.3 The Ébrié Lagoon Fishery, Ivory Coast9.5.3 South and Central American fisheries9.5.3.1 The Gulf of Nicoya Fishery, Costa Rica9.5.3.2 The Cienaga Grande de Santa Marta Fishery, Columbia9.5.3.3 The fisheries of Lake Maracaibo, Venezuela9.5.3.4 The Valenca Delta Fishery, Brazil9.5.4 Australasian fisheries9.5.4.1 Lates calcarifer fisheries of Australia and Papua New Guinea9.5.5 European and North American fisheries9.6 The main fishery species in Europe and North America9.6.1 Diadromous species9.6.2 Marine seasonal migrants as adults9.6.3 Marine migrants as juveniles9.6.4 Estuarine-resident species9.7 Connectivity9.8 Concluding remarks9.9 Acknowledgements9.10 ReferencesChapter 10: Conservation of Estuarine Fishes10.1 Introduction10.2 Analysis of threats to estuarine fish conservation10.2.1 Fisheries10.2.2 Habitat alteration/loss10.2.3 Water quality and quantity alterations10.2.4 Climate change10.2.5 Non-native species10.3 Conservation interventions and instruments10.3.1 Legislative frameworks10.3.1.1 International initiatives10.3.1.2 Regional initiatives10.3.1.3 National initiatives10.3.1.4 Environmental non-governmental organisations10.3.2 Role of protected areas10.3.3 Rehabilitation and habitat restoration10.3.4 Catchment conservation10.3.5 Captive breeding and stocking10.4 Threatened species and extinction risk: some case studies10.4.1 Estuarine pipefish Syngnathus watermeyeri10.4.2 Ganges shark Glyphis gangeticus10.4.3 Totoaba Totoaba macdonaldi10.4.4 European eel Anguilla anguilla10.4.5 Cape stumpnose Rhabdosargus holubi10.5 Current and future challenges10.6 Conclusions10.7 Acknowledgements and dedication10.8 ReferencesChapter 11: Non-native Species in Estuaries11.1 Introduction11.2 What conditions favor non-native species in estuaries?11.2.1 Overview11.2.2 San Francisco Estuary11.2.3 Baltic Sea11.2.4 Chesapeake Bay11.2.5 Tagus Estuary11.2.6 South African estuaries11.2.7 Overview11.3 What are the characteristics of successful non-native estuarine fishes?11.3.1 General characteristics11.3.2 Taxonomy11.3.3 Mode of introduction11.4 Do non-native species become integrated into the biota of estuaries?11.4.1 Alternatives to species invasions11.4.2 Novel species, novel ecosystems11.4.3 Overview11.5 How should non-native species in estuaries be managed?11.6 How do non-native fishes fit into estuarine ecosystems?11.7 Conclusions11.8 Acknowledgements11.9 ReferencesChapter 12: Management of Fishes and Fisheries in Estuaries12.1 Introduction12.2 Management background, aims and philosophies12.2.1 Background and basis for management12.2.2 Environmental Quality Objectives and sustainable management12.2.2.1 Indicators and monitoring as tools in management12.2.3 Information for estuarine management12.2.3.1 Information needs and communicating management issues12.2.3.2 Information and data production, use and dissemination12.2.4 Case studies of priority issues for management12.2.4.1 Australia12.2.4.2 Humber (UK)12.2.4.3 United States of America12.3 Management of activities and habitats, monitoring and surveillance12.3.1 Estuarine environmental management12.3.2 Monitoring of activities for management12.3.3 Licencing of plans and projects12.3.4 Cumulative effects assessment12.3.5 Management of recreational fishing12.3.6 Management of habitats12.3.6.1 Management of loss and gain in estuarine habitats12.4 Management approaches at whole catchment and estuary level12.4.1 Management of catchments12.4.2 Whole estuary management approaches12.4.3 Determining if estuarine management is successful12.4.4 Estuarine management: holistic case studies12.4.4.1 New Zealand12.4.4.2 Japan12.4.4.3 South Africa12.4.4.4 Eastern United States of America12.4.4.5 Western United States of America12.5 Management of species and stocks/fisheries12.5.1 Background12.5.2 Management of species and stocks case studies12.5.2.1 United Kingdom12.5.2.2 Baltic Sea12.5.2.3 Australia12.5.2.4 United States of America12.6 Administrative and legal aspects of managing estuarine fish ecology and fisheries12.6.1 Governance background12.6.2 European legislation12.6.2.1 The Water Framework Directive12.6.2.2 Habitat and Species Directive12.6.3 Administrative bodies12.6.3.1 Management authorities: the Humber Estuary, UK example12.6.3.2 Laws and administration: the USA example12.7 Main messages and recommendations for management12.8 Future research into management methods12.9 Acknowledgements12.10 ReferencesChapter 13: Fish and Fisheries in Estuaries: Global Synthesis and Future Research Directions13.1 Introduction – Changing estuarine landscapes: habitats, research and society13.2 What fishes are in estuaries and why?13.3 Estuarine fish recruitment and habitats – connectivity across space and time13.3.1 Gaps in knowledge and future research directions13.4 How much do we really understand about the role of fish in an estuarine food web?13.4.1 Background13.4.2 Fish food resources in estuaries13.4.3 Factors influencing feeding movements, foraging ecology and migrations13.4.4 Trophic categorization13.4.5 Resource partitioning, energy flow and food web complexity13.4.6 Gaps in knowledge and future research directions13.5 Fishes – good indicators of environmental change?13.5.1 Background to the integration of human pressures13.5.2 Fishes as biological indicators13.5.3 Environmental health fish-based indices13.5.4 Disentangling fish responses in the multi-stress context of global changes13.5.5 Gaps in knowledge and future research directions13.6 Climate change and habitat degradation – a double whammy for fish in estuaries?13.6.1 Background13.6.2 Climate change13.6.3 Habitat degradation13.6.4 Gaps in knowledge and future research directions13.7 Estuarine species are invading and shifting their distributions13.7.1 Invasions of non-native species13.7.2 The ebb and flow: geographical expansion and contraction of species13.7.3 Gaps in knowledge and future research directions13.8 The importance and future of fisheries in estuaries – societal goods and benefits?13.8.1 Fisheries management in the future13.9 Estuarine fish conservation for the future13.9.1 Gaps in knowledge and future research directions13.10 Restoring and managing estuaries for fish, fisheries and habitats13.10.1 Management actions for restoring and rehabilitating estuaries13.10.2 Gaps in knowledge and future research directions13.11 Science-for-policy and policy-for-science – role of estuarine ichthyologists?13.12 Fish and fisheries research in estuaries – the way forward13.13 Acknowledgements13.14 ReferencesAppendix 1: Study Methods I - Field Equipment, Sampling and MethodsA1.1 IntroductionA1.2 Sampling methodsA1.2.1 ‘Traditional’ sampling (nets and traps)A1.2.1.1 Trawl netsBeam trawlOtter trawlPelagic trawlOther trawlsA1.2.1.2 Seine netsBeach seineOther seine netsA1.2.1.3 Fixed nets and trapsFyke netFixed net/trap (e.g. salmon and eel traps)Stow netEntangling nets (gill and trammel nets)Drop net and drop trapsPop net and pull-up trapsOther fixed nets and trapsA1.2.1.4 Fishing linesLong linesHand lineA1.2.1.5 Ichthyoplankton samplersVertical and horizontal plankton netsBongo netGulf samplerLarval light trapsA1.2.1.6 Power station screensA1.2.1.7 Hand gathering methodsGlass eel tow net and elver dip netPush netKick samplingA1.2.2 Visual and acoustic methodsA1.2.2.1 Visual detectionDivingUnderwater videoA1.2.2.2 Acoustic detectionHydroacousticsAcoustic camerasAcoustic telemetryA1.2.2.3 Other observation techniquesA1.2.3 Environmental DNA methodsA1.2.3.1 DNA analysisDNA and eDNA methodsTargeted PCR methodsHigh-throughput sequencingA1.2.3.2 Strengths and disadvantages of DNA-based methodsFeasibility and costseDNA and the possible presence of an organism in that environmentCan eDNA provide quantitative information?DNA techniques for environmental monitoringA1.3 Factors influencing the design of fish monitoring programmesA1.3.1 Monitoring techniquesA1.3.2 Spatial considerationsA1.3.3 Temporal considerationsA1.3.4 A decision tree for monitoring, surveillance and survey designA1.3.4.1 Decision level 1: definition of main questions and hypothesesA1.3.4.2 Decision level 2: monitoring definitionA1.3.4.3 Decision level 3: types of survey required/desiredA1.3.4.4 Decision level 4: associated parameters/integrated monitoringA1.3.4.5 Decision level 5: methods to be used in monitoringA1.4 AcknowledgementsA1.5 ReferencesAppendix 2: Study Methods II - Data Processing, Analysis and InterpretationA2.1 IntroductionA2.2 Individual levelA2.2.1 SizeA2.2.2 Age/growth determination (otoliths/scales)A2.2.3 Diet and stomach analysesA2.2.3.1 Prey selectivity and prey importanceA2.2.4 Sex/gonad development (Gonadosomatic Index)A2.2.5 External bodies abnormalities and fish healthA2.2.6 Toxins and bioaccumulationA2.3 Population levelA2.3.1 AbundanceA2.3.2 BiomassA2.3.3 Condition, disease, parasitism, and liver somatic indexA2.3.4 Genetic structureA2.3.5 Cohort analysisA2.3.6 Growth, mortality rates and modelsA2.3.7 ProductionA2.3.7.1 Biological productionA2.3.7.2 Fisheries productionA2.3.8 Yield modelsA2.3.9 Use of fishery statisticsA2.4 Community levelA2.4.1 Community structureA2.4.2 Multi-metric fish-based indicesA2.5 General analysis methods and the role of modelsA2.5.1 The types and roles of numerical modelsA2.6 Precision versus accuracy – Analytical Quality Control/Quality AssuranceA2.7 Concluding commentsA2.8 AcknowledgementsA2.9 ReferencesFish Species IndexGeographical IndexGeneral Index