Year-round nitrate measurements over a 16-year period from precipitation, groundwater, two harbors, Cape Cod Bay, and Buzzards Bay have been analyzed for their long-term nitrate cycles and correlations. Cyclic behavior in annually averaged nitrate concentration at variable amplitude and periodicity was observed in both estuaries, in the bays, and in the groundwater. These five nitrate concentration time series had correlations of 0.7 or larger among themselves and, except for Cape Cod Bay, with the annually averaged water table height upgradient of the two harbors. The low-frequency water table height variation explained 50% or more of the harbor nitrate variability. The nitrate concentrations were also correlated with the averaged wintertime precipitation amount in the area that had similar multi-year variability. These low-frequency correlations were found to be regional in nature and were thought to be from changes in hydraulic head caused by climatic scale changes in precipitation and infiltration. This was likely driven by changes in the winter hydrological cycle and was decoupled from seasonal scale events. The contribution that the new data in this study make comes from their regular sampling intervals, extended duration, and analyses at climatic scales.