Improvements in Chesapeake Bay water quality and habitat depend on reductions of nutrient and sediment loads. To assist EPA’s Chesapeake Bay Program Office in tracking stressors to the Bay, we calculated 1990-2004 annual nitrogen and phosphorus loads using a new method that includes estimates from portions of the watershed where regular monitoring programs are not feasible. Estimated median total loads for nitrogen and phosphorus were 140 Mg yr^-1 (yield 8.4 kg ha^-1 yr^-1) and 6.4 Mg yr^-1 (0.38 kg ha^-1 yr^-1) respectively. Non-tidal, nonpoint sources composed the greatest proportion of nitrogen (55%) and phosphorus (47%) loads. Unmonitored tidal, nonpoint sources (i.e., coastal plain) contributed 25 and 32% (nitrogen and phosphorus respectively) of total loads. Yields of tidal, non-point loads for nitrogen (9.3 kg ha^-1 yr^-1) and phosphorus (0.49 kg ha^-1 yr^-1) were elevated compared to nontidal areas. Nitrogen loads related linearly to total discharge to the Bay whereas phosphorus loads did not. These methods generated valuable stress indicators for the Chesapeake Bay. Loads originating from tidal, nonpoint areas appeared to contribute proportionately more (by area) to the Bay’s total nutrient loads. Restoration efforts need to reduce non-point source contributions from the watershed above and below the line of tide.