1. Worldwide, water regulatory structures have impacts on aquatic ecological connectivity. This study determined the effects of current sluice management on the fish community in the Baral River, a major connection to the largest wetland (Chalan Beel) in Bangladesh. It also examines wider problems for biodiversity conservation (particularly waterbirds) in that wetland, which has shrunk to 30% of its former dry‐season size in 50 years.
2. During the flood period, the peak breeding time for native floodplain fishes, sluices were in undershot operation (open by 16–60% of water depth). During this time, fish abundance and species richness were 229% and 155% higher respectively at sites upstream of the sluices, despite similar habitat upstream and downstream. Outside this period, when sluices were fully open, abundance and species richness were similar upstream and downstream.
3. Fish samples were dominated by fry, which are susceptible to damage by sluices. Twenty (41.7%) of 48 fish species captured in this study are classed as threatened in Bangladesh and their abundance was significantly lower downstream of the sluices. Two alien species, Aristichthys nobilis and Hypophthalmichthys molitrix, were recorded, probably escapees from local aquaculture activities.
4. Twenty‐five species of wetland birds were recorded in the Chalan Beel. From interviews, 64% of these species appear to have decreased in the last 20 years, together with 11 more species that may have become locally extinct over this period. This suggests that widespread ecological disruption is occurring.
5. Improved water management (e.g. gate opening height and duration) or modification (e.g. fish pass) of the Baral sluices is needed, to meet biodiversity and fisheries needs, rather than just for flood control and crop production. Improved hydrological and ecological connectivity and habitat protection are needed, as are a cessation of destructive fishing and seasonal fish ranching practices that currently provide synergistic pressures.