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.
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