The Salish sucker (Catostomus sp. cf. catostomus) is a federally Threatened species under Canada’s Species at Risk Act and is restricted to 11 watersheds in British Columbia (lower Fraser River Valley) and six in Washington State. Agricultural development has been historically prominent in these areas, and hypoxia and the physical destruction of habitat have been identified as the most important threats to this species. Synergistic effects of reduced streamflow, nutrient inputs, and high temperatures are likely large determinants of seasonal hypoxia. The effects of stream flow on temperature and dissolved oxygen in Salish sucker critical habitat, and corresponding changes in habitat use, distribution, and growth of Salish sucker were studied. As salmonids are even more sensitive to impaired water quality than suckers, and maintaining salmonid populations is an additional major conservation concern in the lower Fraser Valley, the biological response of juvenile coho salmon was also studied as they co-occur in Salish sucker habitats. Through various flow manipulation and enclosure experiments I found that severely reducing flow in off-channel ponds resulted in low levels of dissolved oxygen (< 3 mg·L-1). Salish sucker showed variable growth rate differences in flow and no-flow treatments, while juvenile coho salmon showed significantly decreased growth under the no flow treatment. A subset of fish were tagged with a passive integrated transponder (PIT), and their movement into an enclosed oxygenated refuge was studied. Salish sucker and coho salmon both made greater use of the oxygenated refuge under the no flow treatment. Salish sucker use of the oxygenated refuge was highest at night. It is likely that the availability of an oxygenated refuge in all treatments mitigated negative impacts of reduced water quality on Salish sucker. The results of my thesis will help inform the potential costs and benefits of flow reduction or flow enhancement, and the potential impacts of altered flows in a changing climate.