Nitrogen pollution of waterways is a large global problem, particularly in regions with intensive cropland agriculture, such as the Mississippi River Basin. Unlike prior studies based on agronomic and hydrologic (ag-hydro) models, we collect detailed data from water quality monitors and employ panel data econometric methods to estimate the relationship between cropland and nitrogen pollution. We find an increase in nitrogen load in nearby downstream waterways associated with an additional corn acre upstream that is substantially smaller than the field-to-river adjusted loss per cropland acre based on ag-hydro models. Our findings are consistent with those of recent research documenting the accumulation of large amounts of nitrogen in subsurface soil and groundwater over several decades; this is surplus nitrogen that was applied to fields but has yet to appear in waterways. This legacy nitrogen eventually reaches streams and rivers exacerbating further nitrogen pollution leading to time lags in measurable water quality improvements following the implementation of mitigation practices and policies. In the presence of large amounts of legacy nitrogen, land retirement, and other on-farm mitigation practices, may not be cost effective. Downstream off-farm practices, such as the development of fluvial wetlands, which remove both legacy and new nitrogen, can be cost-effective.