The spatial and temporal variability of sea surface temperature (SST) and Chlorophyll-a (Chl-a) in the Gulf of Maine (GOM) is examined using daily, cloud-free Data INterpolating Empirical Orthogonal Function (DINEOF) reconstructions during 2003–2012. The utility of the DINEOF SST and Chl-a is demonstrated through direct comparisons with buoy- and ship-based observations. EOF analyses of cloud-free products are further used to quantify the SST and Chl-a variability on seasonal to inter-annual timescales. The first mode of SST is dominated by an annual cycle in response to net surface heat flux, with SST lagging surface flux by ~57days. The second mode of SST underscores interactions between GOM, the Scotian Shelf, and the slope sea in response to the basin scale atmospheric forcing represented by the North Atlantic Oscillation. The third mode correlates well with the evolution of Scotian Shelf-slope frontal displacement. The first EOF mode of Chl-a is dominated by a winter–spring bloom and a fall bloom, with a spatial distribution modified by the tidal mixing that facilitates nutrient delivery from the deep ocean. The second EOF mode is likely associated with a winter bloom in the warm slope sea, where the low-frequency variations of second modes of SST and Chl-a are in phase, suggesting a possible coupling between physical and biological responses to atmospheric forcing. The third mode of the Chl-a is likely associated with freshening events associated with advection of the Scotian Shelf Water, which enhance stratifications in the eastern GOM. •Satellite SST and Chl-a in the Gulf of Maine are reconstructed using DINEOF.•Reconstructed data are in good agreement with in situ observations.•Major modes of variability are further examined based on EOF decomposition.•Low frequency variations are likely associated with the North Atlantic Oscillation.