We studied nutrient sources to the Sacramento River and Suisun Bay (northern San Francisco Bay) and the influence which these sources have on the distributions of dissolved inorganic nitrogen (DIN) and dissolved reactive phosphorus (DRP) in the river and bay. We found that agricultural return flow drains and a municipal wastewater treatment plant were the largest sources of nutrients to the river during low river flow. The Sutter and Colusa agricultural drains contributed about 70% of the transport of DIN and DRP by the river above Sacramento (about 20% of the total transport by the river) between August 8 and September 26, 1985. Further downstream, the Sacramento Regional Wastewater Treatment Plant discharged DIN and DRP at rates that were roughly 70% of total DIN and DRP transport by the river at that time. Concentrations at Rio Vista on the tidal river below the Sacramento plant and at the head of the estuary were related to the reciprocals of the river flows, indicating the importance of dilution of the Sacramento waste by river flows. During very dry years, elevated DIN and DRP concentrations were observed in Suisun Bay. We used a steady-state, one-dimensional, single-compartment box model of the bay, incorporating terms for advection, exchange, and waste input, to calculate a residual rate for all processes not included in the model. We found that the residual for DIN was related to concentrations of chlorophylla (Chla). The residual for DRP was also related to Chla at high concentrations of Chla, but showed significant losses of DRP at low Chla concentrations. These losses were typically equivalent to about 80% of the wastewater input rate.