Human driven alterations to the flow of the Snake River and stocking of nonnative rainbow trout (Oncohynchus mykiss) have compromised natural ecosystem processes and native species metapopulations. The Fort Hall Bottoms within the Fort Hall Indian Reservation of the Shoshone-Bannock Tribes (Idaho, USA), is a testament to these challenges. This culturally significant landscape is one of the few physically intact river-floodplain ecosystems remaining in the Snake River Basin. For over a decade, the Fort Hall Bottoms has seen a major reduction in the floodplain’s natural flood regime due to the manipulations of the rivers outside reservation boundary lines. This reduction has led to a decline in suitable habitat for spawning of local species such as the Yellowstone cutthroat trout (Oncorhynchus clarkii bouvieri) due to the lack of natural riverbed scouring. To address this issue, the Shoshone-Bannock Tribal Fish and Wildlife Department implemented localized habitat manipulations to enhance stream habitats to increase fish abundance. We evaluated the before and after trends of trout abundance at two treated and one control site, by boat electrofishing and snorkel surveys. Preliminary results suggest there may not be detectable effects of habitat manipulation on localized trout abundance, but our analyses are ongoing. Across all sites, fish assemblages are dominated by rainbow trout and rainbow trout x Yellowstone cutthroat trout hybrids. Another dimension of this study is to investigate the proportions of the rainbow trout present at these sites that were stocked in nearby waters but have crossed reservation boundaries, and how this may be mediating any prospective responses by native Yellowstone cutthroat trout. We are also using population modeling to evaluate potential impacts of rainbow trout on Yellowstone cutthroat trout. Our preliminary analyses suggest that localized habitat manipulations alone may not be adequate to meet the management goals of the Tribes. Rather, more challenging efforts that address issues beyond reservation boundaries, such as negotiating changes in the regulation of Snake River flows or alterations in stocking practices in the river and downstream reservoir, may be required. The outcomes of our investigations are intended to help the Tribal community identify management priorities for the coming years.