Abrupt changes in flow regimes, particularly those associated with dam operations, can have significant ecological consequences. These impacts are especially pronounced in systems with complex floodplain habitats, where abrupt flow reductions can disrupt connectivity and ecological function. Over half of the world’s largest rivers face this problem, and yet there is no simple solution to minimize the impact on downstream aquatic habitats. In the Upper Snake River, below Jackson Lake Dam, water and resource managers seek recommendations for ramp-down protocols that result in less stranding and loss of native fish (e.g., cutthroat trout) and macroinvertebrates. Addressing this problem is challenging due to the complex relationship between the aquatic ecosystem, dynamic floodplain topography, hydrology, and water management. We address this by using a team-based approach to synthesize existing hydrologic, topographic, ecological and remotely sensed data for the river segment, develop and validate inundation models, and assess the ecological impacts associated with two years of ramp-down regimes. Our results will generate expectations of responses to different flow management scenarios that can be used in water management decision-making. Are there particular flows where higher rates of habitat loss occur? During the first year of the study, we observed substantial stranding of macroinvertebrates and non-salmonid larval fishes. While no large-scale effects on cutthroat trout were observed during this year’s ramp-down, we anticipate indirect impacts due to the loss of macroinvertebrates as a critical food source. These findings are integral to refining our understanding of the ecological consequences of abrupt flow changes and guiding the development of management strategies to mitigate these impacts. Our goal is to inform the design of modified ramp-down protocols that minimize ecological disruptions while meeting water management objectives. By improving flow management practices, we aim to enhance the resilience and sustainability of the Upper Snake River’s aquatic ecosystems.