AbstractThe 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.