The spatial and temporal water quality dynamics in the last free-flowing watershed draining the western Sierra Nevada were investigated with the aim of establishing a criterion for comparison to analogous impounded watersheds. This study examines the effects of flow regulation on water quantity and quality by comparing an impounded system (Mokelumne River) with an adjacent unimpounded system (Cosumnes River). Water quality in the Cosumnes River displays a strong seasonal cycle with nearly the entire annual load of TSS, nitrate, and phosphate being exported during the stormflow season (Nov. – Mar.). The meltflow season (April – June) is marked by high discharges of dilute water, while the baseflow season (July – Oct.) is determined by groundwater chemistry that is characterized by median levels of dissolved salts. This seasonal cycle is not seen in the adjacent Mokelumne Watershed where the Pardee-Camanche Reservoir System impounds 0.73 km2 of water, buffering seasonal cycles and altering effluent chemistry. The reservoirs act as sinks of most constituents analyzed, except Chlorophyll-a, phosphate, and nitrate – inverting inflowing nitrate patterns the reservoirs tend to depress stormflow nitrate peaks and elevate nitrate levels during the melt and baseflow seasons, resulting in a net annual export. The reservoir dynamics which cause this temporal shift in the nitrate chemograph are disconnected from the landscape influences which drive seasonal water quality dynamics in the Cosumnes. Stream water sediment and nitrate loading across the Cosumnes Watershed is controlled by a combination of population density, extent of agriculture, rainfall, and grassland coverage. As population density and agriculture increase so does sediment and nitrate export. Grasslands have a more complex relation with nitrate loading – during wet years grasslands produce nitrate, but during dry years the waterways in the subwatersheds dominated by grass tend to act as nitrate sinks. Major dams, similar to those found on the Mokelumne, exist on 19 of the 20 rivers that drain into the Central Valley of California. The results of this study suggest that the ubiquity of large impoundments in California has drastically altered the spatiotemporal chemical dynamics of downstream waterways.