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The TRRP aims to restore salmonid habitat for population recovery through mechanical restoration and flow management targeted in the 64-km reach below Lewiston Dam, known as the restoration reach. Restoration strategies are intended to evolve through adaptive management regarding habitat assessment, restoration action, and rehabilitation effectiveness monitoring. This report synthesizes data collected in the Trinity River restoration reach for flows, physical terrain, hydraulics, and fish distribution. These data informed the development of a spatially explicit, flow specific hydrodynamic fish capacity model we used to assess TRRP’s efforts to rehabilitate habitat for juvenile Chinook Salmon (Oncorhynchus tshawytscha). Rehabilitated areas had greater capacity than non-rehabilitated areas in four out of seven hydrologically distinct sub-reaches. Evaluation of capacity-flow relationships between sub-reaches and rehabilitation sites showed that capacity was generally greater in upstream areas compared to downstream areas. Reach-scale fry and presmolt capacity was positively related to topographic complexity within the active channel and to wetted width. We concluded that confined wetted width limits physical capacity in downstream sub-reaches, likely due to planform setting affected by mine tailings and subsequent incision. Under current management, winter baseflow limits capacity during 70% of the rearing period, especially for the fry life stage, and we found that fry capacity tends to be limited over a wider and more frequent range of flows in downstream reaches. Throughout the entire restoration reach, increasing baseflow to 14.2 m3/s decreases capacity by 7%, but increasing baseflow to 28.3 m3/s, 42.5 m3/s or 56.7 m3/s would increase capacity by 2%, 18% or 25%, respectively, during the rearing period. We recommend rehabilitation efforts prioritize increasing topographic complexity within the active channel and designing features that increase wetted width at discharges that occur for long durations during the critical rearing period to facilitate juvenile salmonid rearing. We also recommend that alternative flow management during the critical rearing period be evaluated for its role in alleviating habitat bottlenecks for fry and presmolt life stages in winter and spring.