The continental shelf of the West Antarctic Peninsula (WAP) is characterized by strong along‐shore hydrographic gradients resulting from the distinct influences of the warm Bellingshausen Sea to the south and the cold Weddell Sea water flooding Bransfield Strait to the north. These gradients modulate the spatial structure of glacier retreat and are correlated with other physical and biochemical variability along the shelf, but their structure and dynamics remain poorly understood. Here, the magnitude, spatial structure, seasonal‐to‐interannual variability, and driving mechanisms of along‐shore exchange are investigated using the output of a high‐resolution numerical model and with hydrographic data collected in Palmer Deep. The analyses reveal a pronounced seasonal cycle of along‐shore transport, with a net flux (7.0 × 105 m3/s) of cold water toward the central WAP (cWAP) in winter, which reverses in summer with a net flow (5.2 × 105 m3/s) of Circumpolar Deep Water (CDW) and modified CDW (mCDW) toward Bransfield Strait. Significant interannual variability is found as the pathway of a coastal current transporting Weddell‐sourced water along the WAP shelf is modulated by wind forcing. When the Southern Annual Mode (SAM) is positive during winter, stronger upwelling‐favorable winds dominate in Bransfield Strait, leading to offshore advection of the Weddell‐sourced water. Negative SAM leads to weaker upwelling‐ or downwelling‐favorable winds and enhanced flooding of the cWAP with cold water from Bransfield Strait. This process can result in significant (0.5°C below 200 m) cooling of the continental shelf around Palmer Station, highlighting that along‐shore exchange is critical in modulating the hydrographic properties along the WAP.