Anthropogenic development has adversely affected river habitat and species diversity in urban rivers, and existing habitats are jeopardized by future uncertainties in water resources management and climate. The Los Angeles River (LAR), for example, is a highly modified system that has been mostly channelized for flood control purposes, has altered hydrologic and hydraulic conditions, and is thermally altered (warmed), which severely limits the habitat suitability for cold water fish species. Efforts are currently underway to provide suitable environmental flows and improve channel hydraulic conditions, such as depth and velocity, for adult fish migration from the Pacific Ocean to upstream spawning areas. However, the thermal responses of restoration alternatives for resident and migrating cold water fish have not been fully investigated. Using a mechanistic model, we simulated the LAR’s water temperature under baseline conditions and future alternative restoration scenarios for migration of the native, anadromous steelhead trout in Southern California and the historically resident Santa Ana sucker. We considered three scenarios: 1) increasing roughness of the low-flow channel, 2) increasing the depth and width of the low-flow channel, and 3) allowing subsurface inflow to the river at a soft bottom reach in the LA downtown area. Our analysis indicates that the maximum weekly average temperature (MaxWAT) in the baseline condition was 28.9°C, suggesting that the current river temperatures would act as a limiting factor during the steelhead migration season and habitat for Santa Ana sucker. The MaxWAT dropped about 3%–28°C after applying all the considered scenarios at the study site, which is 3°C higher than the determined steelhead survival threshold. Our simulations suggest that without consideration of thermal restoration, restoring hydraulic conditions may be insufficient to support cold water fish migration or year-round resident native fish populations, particularly with potential river temperature increases due to climate change.