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Abstract The American cranberry ( Vaccinium macrocarpon Ait.) is an important part of the cultural heritage and economy of Southeastern Massachusetts, yet water quality concerns and wetland protection laws challenge its commercial production. Here, we report inputs and outputs of water, nitrogen (N), and phosphorus (P) for a 2.12‐ha cranberry bed over a 2‐year period from 2013 to 2015. Water‐budget analysis indicated that precipitation contributed 40%, floodwater 37%, irrigation 15%, and groundwater 8% of water inputs to the cranberry bed. Minor annual variation in surface water discharge (~90 mm·year −1 or 3%) contrasted with large decreases in net (= outputs − inputs) nutrient export, from 16.2 to 9.1 kg N·ha −1 ·year −1 for total (dissolved + suspended particulate) nitrogen (TN) and from 3.34 to 1.47 kg P·ha −1 ·year −1 for total phosphorus (TP) between Years 1 and 2. Annual variation in net TN and TP export was tied to decreases in spring and summer nutrient export and controlled by the combined effects of fertilizer management, soil biogeochemistry, and hydrology. The relatively high spring TN export in Year 1 was associated with coincident increases in soil temperature and rainfall. A second factor was the timing of fertilizer application, which occurred 1 day prior to a major summer storm (i.e., third largest daily rainfall since 1926) and was responsible for up to 15% and 9% of the Year 1 TN and TP export, respectively. Nutrient budgets, which balanced water and fertilizer inputs with water, fruit, and vegetative outputs, were consistent with the burial of 21.6 kg N·ha −1 ·year −1 and 7.27 kg P·ha −1 ·year −1 . Field measurements indicated that burial would increase TN and TP in the shallow (0–5 cm) rooting zone by 14% and 6%, respectively, which seemed plausible based on the relatively young age of the bed (4–5 years) and new root growth patterns in Vaccinium plants.