The steep US Virgin Islands Shelf Break (VISB) and the Virgin Islands Trough (VIT) at the Northeastern Caribbean Sea comprise a dynamic region of the Atlantic Ocean. In situ oceanographic data collected in the region during April 2017 were used to examine the spatial variability in temperature, density, salinity, and relative Chlorophyll-a. Analysis of data from the upper 300 m of the water column, that include deep and shallow water stations in the shelf break region, shows strong stratification of the water column. Stations shallower than 800 m along the shelf break are more variable in temperature, density, and salinity than those that are deeper than 800 m along the trough. For shallow stations, the mixed layer depth deepens along-shelf from West to East while at the deep stations the opposite occurs. Salinity maxima exhibit more variability in depth and range of values in the shallow stations compared to deep stations. Six different types of water masses that contribute to the strong stratification in the region were identified in our study: Caribbean Surface Water, Subtropical Underwater, Sargasso Sea Water, Tropical Atlantic Central Water, Antarctic Intermediate Water, and North Atlantic Deep Water. The upper level Caribbean Surface Water, Subtropical Underwater, and Sargasso Sea Water are present in shallow stations, indicating potential meridional intrusions from the VIT to the VISB which may not be resolved by current ocean circulation models and are not captured in satellite data. The analysis presented here indicates that competing physical processes may be controlling the vertical structure of the water column in the region and merit further examination.