Elevated nitrogen concentrations in streams and rivers in the Chesapeake Bay watershed have adversely affected the ecosystem health of the bay. Much of this nitrogen is derived as nitrate from groundwater that discharges to streams as base flow. In this study, boosted regression trees (BRTs) were used to relate nitrate concentrations in base flow (n = 156) to explanatory variables describing nitrogen sources, geology, and soil and catchment characteristics. From these relations, a BRT model was developed to predict base flow nitrate concentrations in streams throughout the Chesapeake Bay watershed. The highest base flow nitrate concentrations were associated with intensive agricultural land use, carbonate geology, and sparse riparian canopy, which suggested that reduced nitrogen inputs, particularly over carbonate terrane, are critical for limiting nitrate concentrations. The lowest nitrate concentrations in the BRT model were associated with extensive riparian canopy, high levels of organic carbon in soils, and suboxic conditions at shallow depths, which suggested that denitrification in the subsurface, particularly in the riparian zone, is limiting base flow nitrate concentrations. Nitrate transport from aquifers to streams can take decades to occur, resulting in decades-long lag times between the time when a land-use activity is implemented and when its effects are fully observed in streams. Predictive models of base flow nitrate concentrations in streams will help identify which portions of a watershed are likely to have large fractions of total stream nitrogen load derived from pathways with significant lag times.