We developed, and applied in two sites, novel methods to measure ground water-borne nitrogen loads to receiving estuaries from plumes resulting from land disposal of waste water treatment plant (WWTP) effluent. In addition, we quantified nitrogen losses from WWTP effluent during transport through watersheds. WWTP load to receiving water was estimated as the difference between total measured ground water-transported nitrogen load and modeled load from major nitrogen sources other than the WWTP. To test estimated WWTP loads, we applied two additional methods. First, we quantified total annual waste water nitrogen load from watersheds based on nitrogen stable isotopic signatures of primary producers in receiving water. Second, we used published data on ground water nitrogen concentrations in an array of wells to estimate dimensions of the plume and quantify the annual mass of nitrogen transported within the plume. Loss of nitrogen during transport through the watershed was estimated as the difference between the annual mass of nitrogen applied to watersheds as treatment plant effluent and the estimated nitrogen load reaching receiving water. In one plume, we corroborated our estimated nitrogen loss in watersheds using data from multiple-level sampling wells to calculate the loss of nitrogen relative to a conservative tracer. The results suggest that nitrogen from the plumes is discharging to the estuaries but that substantial nitrogen loss occurs during transport through the watersheds. The measured vs. modeled and stable isotopic approaches, in comparison to the plume mapping approach, may more reliably quantify ground water-transported WWTP loads to estuaries.