Long-term monitoring data from freshwater lakes can be challenging to retrieve yet are valuable for assessing lakes at risk of saltwater intrusion. We demonstrate the use of an applied paleolimnological method to identify the response of a freshwater lake to seawater incursion and salinity-induced meromixis by examining the geochemistry of lake sediments deposited over the past century. Laytons Lake is located 1.5 km from the Bay of Fundy coastline, and experienced documented seawater incursion events in 1944 and 1949 leading to a period of extended meromixis (>40 yr). Our limnological measurements indicate that meromixis no longer exists at Laytons Lake, and hypolimnetic phosphorus (P) concentrations and conductivity values have declined since 1982. Meromictic conditions, the establishment of the chemocline, and high sedimentation rates collectively preserve a geochemical record of seawater incursion, which was identified as a short-duration, positive chloride (Cl-) excursion followed by the precipitation of iron sulfide (FeS2). A decline in Cl- concentration after the incursion events in the paleorecord may represent the deterioration of the chemocline, and the reestablishment of thermal stratification and mixing. We suspect that seawater incursions can have a multidecadal impact on aquatic systems, and that bulk geochemical analysis of paleolimnological records is a useful, low-cost tool that can provide a long-term perspective on the limnological consequences of such events. These long-term data can inform the assessment of aquatic systems at risk of saltwater incursion due to sea-level rise.