Abrupt changes in flow regimes, particularly those associated with dam operations, can have significant ecological consequences. While many environmental flow alterations work toward endpoints such as maintaining base flows, less work has been done on the transition between high and low flows in manipulated systems. These impacts are especially pronounced in systems with complex floodplain habitats, where abrupt flow reductions can disrupt connectivity and ecological function. The Upper Snake River (Wyoming, USA), below Jackson Lake Dam, is reduced annually from high summer flows to winter base flows over 4-5 days, restricting available aquatic habitat and stranding fish and macroinvertebrates in side channels. Water and resource managers seek recommendations for fall ramp-down protocols that result in less stranding and loss of native fish (e.g., cutthroat trout) and macroinvertebrates. We address this complex problem by using a cross-disciplinary approach that utilizes both hydrological modeling and ecological investigations to assess the impacts associated with two different years of scheduled ramp-down events. Are there rates of change or ranges of flows at which more mortality and habitat loss occur? During the first and second year of the study, we observed substantial stranding of non-salmonid larval fishes and macroinvertebrates, on the order of thousands and hundreds of thousands of individuals, respectively. While no major direct effects on cutthroat trout were observed during either ramp-down, we anticipate and are assessing indirect impacts due to the loss of larval fishes and macroinvertebrates as critical food sources. Preliminary analyses suggest a disproportionate concentration of stranded fishes and macroinvertebrates in side channel habitats. Our analyses of potential differences in responses between the two years are ongoing. By improving flow management practices, we aim to enhance the resilience and sustainability of the Upper Snake River’s aquatic ecosystems.