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Bio-optically, surface waters of the northeastern US continental shelf are strongly heterogeneous, exhibiting highly variable distributions in both time and space of suspended sediment, colored dissolved organic matter (CDOM), and phytoplankton concentration and community structure. These render the standard global NASA satellite chlorophyll algorithm suspect. However, spectral signatures of the water are well quantified by the actual satellite-based multispectral reflectance (Rrs) measurements. Here, we use 6 bands of Rrs measurements from 19 years (1998-2016) of monthly composite SeaWiFS and MODIS data to identify the spectral signatures of dominant water types present over the northeast shelf. A merged multivariate clustering approach that incorporates neural network-based Self-Organizing Maps and agglomerative hierarchical clustering is used to group similar spectral signatures across the entire time and space domain. These sort the surface water into 8 dominant groups. Remapped results provide a climatological view of seasonal cycles of these bio-optical groups and their spatial geography and then quantify their interannual variability over 19 years. Results indicate the same 2-3 spectral groups dominate the study area each year. Several less spatially predominant groups are present mainly along the coast and over George’s Bank. Spectral signatures of the water groups suggest that three groups represent the clearest waters and two groups the most particle and absorption dominated waters, with other groups representing varying concentrations of CDOM and phytoplankton. These descriptions are consistent with both the geographic position of the groups and calculated inherent optical properties of the groups. Interannual variability of the groups at each location effectively captures boundaries between ecological regions, reflecting frontal zones reported in the literature. Quantified trends in the spatial coverage of the groups over the 19 years shows a significant decline in the time/space coverage of the clearest water groups. These trends are strongest and significant in summer months, consistent with strong summer trends in sea surface temperature. There are also systematic trends in water groups in March and May on either side of the April spring bloom, suggesting phenology shifts in bloom characteristics. Over interannual time scales, the more turbid coastal water groups have correlations to wind strength and river discharge. These results provide new satellite-based ocean color measurements of shelf variability over seasonal and interannual time scales and present managers with new tools to monitor biologically important change over this economically critical and rapidly changing ecosystem.