Three-dimensional geological and groundwater flow models of a submarine groundwater discharge (SGD) site at Hanko (Finland), in the northern Baltic Sea, have been developed to provide a geological framework and a tool for the estimation of SGD rates into the coastal sea. The dataset used consists of gravimetric, ground-penetrating radar and shallow seismic surveys, drill logs, groundwater level monitoring data, field observations, and a LiDAR digital elevation model. The geological model is constrained by the local geometry of late Pleistocene and Holocene deposits, including till, glacial coarse-grained and fine-grained sediments, post-glacial mud, and coarse-grained littoral and aeolian deposits. The coarse-grained aquifer sediments form a shallow shore platform that extends approximately 100–250 m offshore, where the unit slopes steeply seawards and becomes covered by glacial and post-glacial muds. Groundwater flow preferentially takes place in channel-fill outwash coarse-grained sediments and sand and gravel interbeds that provide conduits of higher hydraulic conductivity, and have led to the formation of pockmarks on the seafloor in areas of thin or absent mud cover. The groundwater flow model estimated the average SGD rate per square meter of the seafloor at 0.22 cm day⁻¹ in autumn 2017. The average SGD rate increased to 0.28 cm day⁻¹ as a response to an approximately 30% increase in recharge in spring 2020. Sensitivity analysis shows that recharge has a larger influence on SGD rate compared with aquifer hydraulic conductivity and the seafloor conductance. An increase in recharge in this region will cause more SGD into the Baltic Sea.