The US Northeast continental shelf “cold pool” comprises winter-cooled Shelf Water that is trapped below the warm surface layer during the stratified season. The regional ecosystem relies on the preservation of winter conditions within the cold pool throughout the year. Here, we present first evidence of a significant increase in the cold pool’s salt content throughout the stratified season, revealed by sustained multi-year observations from the Ocean Observatories Initiative (OOI) Coastal Pioneer Array (2015-2022) and high-resolution realistic regional model output. Cold pool salinification rates of $0.17\,\mbox{PSU/month}$ remain steady throughout the stratified season, leading to salinity differences of over $1\,\mbox{PSU}$ between March and October. The seasonal onshore movement of the US Northeast shelfbreak front cannot explain the salinity increase since seasonal frontal oscillations are too small and not in phase with the salinification signal. Instead, a cold-pool salinity budget reveals that the observed salinification is caused by an imbalance between cross-shelf salt fluxes, which deposit salt into the cold pool at all times of year, and the strong seasonal cycle of vertical mixing. During the stratified season, vertical mixing shuts down and no longer opposes the cross-shelf flux, leading to net salinification of the cold pool over the summer. Along-shelf freshwater advection from upstream contributes little and is only present in the fall. The strong relationship between the seasonal cycle of cold pool salinification and seasonal stratification points toward the importance of the timing of spring re- and fall de-stratification on near-bottom continental shelf conditions.