Coastal groundwater reserves often reflect a complex evolution of marine transgressions and regressions, and are only rarely in equilibrium with current boundary conditions. Understanding and managing the present-day distribution and future development of these reserves and their hydrochemical characteristics therefore requires insight into their complex evolution history. In this paper, we construct a paleo-hydrogeological model, together with groundwater age and origin calculations, to simulate, study and evaluate the evolution of groundwater salinity in the coastal area of the Netherlands throughout the last 8.5 kyr of the Holocene. While intended as a conceptual tool, confidence in our model results is warranted by a good correspondence with a hydrochemical characterization of groundwater origin. Throughout the modeled period, coastal groundwater distribution never reached equilibrium with contemporaneous boundary conditions. This result highlights the importance of historically changing boundary conditions in shaping the present-day distribution of groundwater and its chemical composition. As such, it acts as a warning against the common use of a steady-state situation given present-day boundary conditions to initialize groundwater transport modeling in complex coastal aquifers or, more general, against explaining existing groundwater composition patterns from the currently existing flow situation. The importance of historical boundary conditions not only holds true for the effects of the large-scale marine transgression around 5 kyr BC that thoroughly reworked groundwater composition, but also for the more local effects of a temporary gaining river system still recognizable today. Model results further attest to the impact of groundwater density differences on coastal groundwater flow on millennial timescales and highlight their importance in shaping today’s groundwater salinity distribution. We found free convection to drive large-scale fingered infiltration of seawater to depths of 200 m within decades ...