The science needed to inform management of environmental flows to temporarily closed estuaries and coastal lagoons is decades behind the state of knowledge for rivers and large embayments. These globally ubiquitous small systems, which are often seasonally closed to the ocean’s influence, are under particular threat associated with hydrologic alteration because of changes in atershed land use, water use practices, and climate change. Managing environmental flows in these systems is complicated by their tight coupling with watershed processes, variable states because of intermittently closing mouths, and reliance on regional scale sediment transport and littoral processes. Here we synthesize our current understanding of ecohydrology in temporarily closed estuaries (TCEs) and coastal lagoons and propose a prioritized research agenda aimed at advancing understanding of ecological responses to altered flow regimes in TCEs. Key research needs include agreeing on a consistent typology, improving models that couple watershed and ocean forcing at appropriate spatial and temporal scales, quantifying stress–response relationships associated with hydrologic alteration, improving tools to establish desired conditions that account for climate change and consider cultural/indigenous objectives, improving tools to measure ecosystem function and social/cultural values, and developing monitoring and adaptive management programs that can inform environmental flow management in consideration of other stressors and across different habitat types. Coordinated global efforts to address the identified research gaps can help guide management actions aimed at reducing or mitigating potential impacts of hydrologic alteration and climate change through informed management of freshwater inflows.

1. Amphidromy is a form of migratory life history typified by the reproduction of fish in freshwater environments, the early downstream dispersal of post-hatch larvae to marine environments, and the return of small-bodied young juveniles to freshwater environments for growth to adulthood. Island freshwater fish communities are frequently dominated by fish species with amphidromous life histories.2. Amphidromous life cycles leave fish communities highly susceptible to habitat modification and disruptions to connectivity across marine and freshwater environments. This means that managing waterway connectivity is fundamental to their conservation; however, the unique and often geographically restricted amphidromous communities that characterize many small island nations have received little consideration in the development of strategies for the management of fish passage.3. The ecology and locomotory capabilities of amphidromous species are often poorly studied, partly because their small size at migratory life stages renders current state-of-the-art in situ biotelemetry methods unsuitable. The small size of fish also means that seemingly small obstructions can severely impede migrations. 4. The steps necessary to advance the management of fish passage for island fish communities are: curating and maintaining barrier inventories; evaluating barrier permeability; developing effective barrier mitigation options; and prioritizing restoration and conservation efforts. 5. New methods for understanding the ecology and locomotory capabilities and behaviour of amphidromous fishes are required to advance the management of fish passage for island fish communities. Fish passage solutions that imitate natural streams, such as those promoted in new guidelines in New Zealand, may be the most effective way of improving waterway connectivity; however, integrated approaches to freshwater fish conservation that account for meta-population dynamics, in combination with the management of fish passage, are necessary to optimize conservation outcomes for amphidromous species.

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Researchers have used laboratory experiments to examine how fish might be affected by anthropogenic alterations and conclude how best to adjust fish passage and culvert remediation designs in response. A common way to document swimming performance for this purpose is measuring fish critical swimming speed (U crit ). Nonetheless, the U crit protocol as defined by Brett [(1964) Journal of the Fisheries Research Board of Canada, 21, 1183-1226] may be inappropriate for studying swimming performance and determining how it relates to upstream migration in benthic fish, as they may not actively swim throughout the entire U crit test. An alternative method to estimate swimming performance is sprint swimming speed (U sprint ), which is suggested to be a measure of the burst speed of fish rather than maximum sustained swimming speed.The authors conducted comparative swimming performance experiments to evaluate whether U sprint can be used to compare swimming performance of benthic species to that of pelagic, actively swimming species. They measured individual swimming speeds of īnanga (Galaxias maculatus), an actively swimming pelagic species, and banded k okopu (Galaxias fasciatus), a fish that exhibits benthic station-holding behaviour, using both the U sprint and U crit test. Experiments revealed that no significant statistical difference between swimming speeds was estimated using the U crit and U sprint test protocols for both G. maculatus and G. fasciatus. The result of this study suggests that fish swimming speeds obtained using these two methods are comparable for the species used in this study. By using U sprint for benthic-associated fish and U crit for pelagic fish, we may be able to compare a broader range of species' swimming abilities for use in a fish passage context.