We identify step-changes in the physical, chemical and biological characteristics of the Gulf of Maine (GoM) using the Gulf of Maine North Atlantic Time Series (GNATS), a series of oceanographic measurements obtained between September 1998 and December 2010 along a transect in the GoM running from Portland, ME, to Yarmouth, NS. GNATS sampled a period of extremes in precipitation and river discharge (4 of the 8 wettest years of the last century occurred between 2005 and 2010). Coincident with increased precipitation, we observed the following shifts: (1) decreased salinity and density within the surface waters of the western GoM; (2) both reduced temperature and vertical temperature gradients in the upper 50 m; (3) increased colored dissolved organic matter (CDOM) concentrations and particle scattering in the western GoM; (4) increased concentrations of nitrate and phosphate across all but the eastern GoM; (5) increased silicate, particularly in the western GoM, with a sharp increase in the ratio of silicate to dissolved inorganic nitrogen; (6) sharply decreased carbon fixation by phytoplankton; (7) moderately decreased chlorophyll, particulate organic carbon (POC) and particulate inorganic carbon (PIC) in the central GoM and (8) decreased POC- and PIC-specific growth rates. Gulf-wide anomaly analyses suggest that (1) the surface density changes were predominantly driven by temperature, (2) dissolved nutrients, as well as POC/PON, varied in Redfield ratios and (3) anomalies for salinity, density, CDOM, particle backscattering and silicate were significantly correlated with river discharge. Precipitation and river discharge appear to be playing a critical role in controlling the long-term productivity of the Gulf of Maine by supplying CDOM and detrital material, which ultimately competes with phytoplankton for light absorption.