Healthy rivers require the interaction of many processes to maintain their functions in ecosystems and human populations. One of these processes is hydrologic exchange flows (HEFs), exchanges between relatively fast-flowing channel waters, with slower- flowing waters off-channel and in the subsurface. Irrigation alters the water quality in HEFs, inputting fertilizers into exchange flows and altering temperature. These HEFs are non-point sources of pollution, making the source of the pollution difficult to identify, especially in large rivers. I identify anomalies in temperature and EC along the streambed as locations of groundwater flux by dragging sensors along the riverbed near the shoreline. I find that inflows are more prevalent during late summer. Late summer is also the driest season of the year. The dry season requires more irrigation water and lower flows in the river cause irrigation runoff to form a larger percentage of the water. Many of these inflows have greater concentrations of nitrate than river water (up to 40 mg N-NO3/L), at levels that are toxic to newly-hatched salmon. These inflows from irrigation are at their peak during salmon spawning season, at which time salmon lay eggs in shallow water. The decreased water quality may limit spawning habitat for returning salmon. I conclude that irrigation runoff negatively impacts ecosystem health and water quality along the shoreline.

Salmon habitat faces many challenges, including polluted irrigation runoff. Irrigation runoff impacts water quality, such as water temperatures and nitrate concentrations. I examine the governance of these water quality parameters using a social-ecological framework that considers the interactions between human activities (irrigation) and the ecosystem (salmon habitat). I found that irrigation runoff is not considered within a social-ecological framework in the governance of the Columbia River. The water quality of irrigation runoff is not managed, allowing farmers to use excess fertilizer which runs into adjacent rivers. I conclude that management of irrigation runoff is important for improvement of shoreline river habitats and suggest that farmers are required to use fertilizer application techniques to prevent polluted runoff.