Discharge of groundwater-derived pollutants to inland and marine coastal waters is influenced by the transport and reactive processes occurring in nearshore aquifers. The effect of shoreline change on these processes and subsequent discharge of pollutants to coastal waters is unclear. The objective of this study was to evaluate the impact of shoreline recession (landward movement of the mean shoreline) on the transport of nitrogen [N] and phosphorus [P] in a nearshore aquifer and their discharge to coastal waters. Field investigations were conducted on a permeable unconfined nearshore aquifer on Lake Huron, Canada, in years coinciding with historically low and high lake water levels. At the site, a septic system-derived nutrient-rich (N and P) groundwater plume is moving towards the lake and the mean shoreline position moved ~30 m landward between sampling years due coastal erosion and mean lake water level increase. Data indicate PO4-P fluxes to the lake were higher following shoreline recession due to shortened travel pathways. In contrast, NO3-N fluxes were governed by the specific geochemical conditions near the sediment-water interface, which are not only a function of the shoreline position. Further, findings show shoreline recession may modify mineral phases that tend to sequester pollutants (e.g., iron oxides) near the sediment-water interface and this may possibly mediate release of sediment-bound pollutants. The findings provide new insights into potential impacts of shoreline change on chemical discharge to coastal waters as needed to inform long-term water quality predictions and management.