Summary This study experimentally quantified the effect of seawater intrusion (salinization) and freshening events in coastal aquifers on nutrient (N, P and DSi) dynamics across the fresh–saline groundwater interface. Laboratory column experiments were conducted under aerobic and anaerobic conditions in order to simulate the processes occurring in the fresh–saline interface. They were performed with aquifer sediments, simulating the natural conditions during alterations of natural fresh groundwater to seawater and vice versa. The salinization and freshening experiments showed that NH4+ and PO43− and DSi were affected mainly by ion exchange processes while microbial activity controlled the nitrogen species NO3− and NO2−. Due to the cation exchange, salinization generated enrichment (above the expected conservative behavior) of NH4+, up to 80 μmol L−1 (an order of magnitude higher than in seawater or fresh groundwater). Under anaerobic conditions NO3− was removed by denitrification, as demonstrated by the decrease in NO3− concentrations, the increase in NO2− concentrations, and the increase in δ15N by 15–25‰. Clear evidence was shown for anion exchange of PO43−, which competes with HCO3− and boron on adsorption sites. DSi seems to take part in the exchange process, similar to PO43−.