When rivers and riverine organisms cross jurisdictional boundaries, management challenges arise. Decisions made about water or organisms in one jurisdiction often constrain those in another. The Snake River in Idaho is one of the most contested waters in the western USA, and one of its only physically intact river-floodplain ecosystems is on the Shoshone-Bannock Tribes’ Fort Hall Reservation. This floodplain encompasses a mosaic of habitats such as large springbrooks, and has strong ecological and cultural importance to the Tribes, including traditional fisheries. Management of dams upstream of the reservation has resulted in loss of the natural flood regime and associated habitat degradation, which the Tribes have attempted to mitigate via localized habitat improvement projects. The native fishes (notably, Yellowstone cutthroat trout Oncorhynchus clarkii bouvieri) found within these Tribal waters also face the challenge of interacting via competition and hybridization with roaming, nonnative rainbow trout (Oncorhynchus mykiss) stocked by the state of Idaho in habitat just outside the reservation. In response to such challenges, we are focusing a collaborative investigation on the following questions: 1) Are localized attempts at habitat improvement positively affecting fish populations, or should focus be directed toward water management to restore floodplain processes? and, 2) To what extent are stocked rainbow trout using Tribal waters, and is this likely to constrain conservation efforts for cutthroat trout? To address these, we are a) evaluating trout population responses to habitat projects via before-after-control-impact comparisons, b) assessing the proportion of triploid rainbow trout relative to Yellowstone cutthroat trout populations through a mark-recapture study and assays of trout reproductive viability, and c) developing models to evaluate possible responses by trout populations to management scenarios. Study findings will be available for the Tribal government to assess current operations and be used for future negotiation and decision making.