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.

The Virgin Islands basin (VIB) includes several Marine Protected Areas (MPAs) of interest as biologically unique spawning aggregation sites. The ecological structure in and around these MPAs is regulated by several factors, including changes in near‐surface water properties. Anomalously low near‐surface salinity is observed in the VIB during April 2009/2011, and March 2010, with a salinity signature consistent with Amazon plume waters. Other low salinity events in the region are found during 2007–2017 using output from an ocean reanalysis. The reanalysis shows that horizontal salinity advection explains near‐surface salinity variability in the VIB to a high degree, including events observed in the in situ measurements. We use a Lagrangian Particle tracking model to track particles over the 2007–2017 period and identify the source and pathways of water imports to the VIB. We describe three pathways. The northernmost one is often associated with advection of salty Atlantic waters. The two southernmost paths are associated with advection of low salinity waters from the Amazon into the VIB. The latter two pathways arrive to the Caribbean Sea as described in previous studies on low salinity advection to the wider Caribbean from the Amazon River; we find that once in the Caribbean Sea, the low salinity water makes its way into the VIB when steered northward by mesoscale features. This results in Amazon River waters regulating salinity variability in the VIB during April–November. During December–March, when mesoscale activity is at its minimum, the Atlantic inflow regulates the salinity variability within the VIB instead.