This is the first well-documented report on the occurrence of pockmarks in Puck Bay. Pockmarks in the seafloor of Puck Bay were discovered during a hydroacoustic survey carried out in 2020. They are located at a depth of 25–27 m in the southwestern part of the bay. Significant depletion of chloride (Cl−) concentrations in sediment pore water was found within the depressions. Most likely, the formation of pockmarks was due to groundwater flow through the Miocene–Pleistocene system of aquifers, which extends from land to the bay area. One-dimensional modeling of vertical Cl− concentration profiles in pore water revealed the upward flow of freshened groundwater within the pockmarks. The magnitude of submarine groundwater discharge (SGD) was estimated to vary from 1.53·10−2 to 18·10−2 L·m−2·h−1. The effect of groundwater seepage was also observed at 3 cm above the seafloor within the pockmarks, which was identified as a decrease in salinity of approximately 0.12 PSU compared to reference sites.Furthermore, due to the effect of water advection, SGD can be detected even several meters above the seafloor as a decrease in salinity values within the thermocline layer.