Intermittently closed and open lakes and lagoons (ICOLLs) are coastal lakes that intermittently exchange water with the sea and experience saline intrusions. Understanding effects of seawater exchange on local biota is important to preserve ecosystem functioning and ecological integrity. Coastal dune lakes of northwest Florida are an understudied group of ICOLLs in close geographic proximity and with entrance regimes operating along a frequency continuum. We exploited this natural continuum and corresponding water chemistry gradient to determine effects of water chemistry on resident submersed aquatic vegetation (SAV) distributions in these ecosystems. SAV distribution decreased with increases in salinity, but was unaffected by variation in nitrogen, phosphorous, and turbidity. Salinity perturbations corresponding with water exchange with the Gulf of Mexico were associated with reductions in SAV in coastal dune lakes. Potential impacts associated with changes in global climate may increase the frequency of seawater exchange across all coastal dune lakes and potentially reduce the distribution of oligohaline macrophytes among these ecosystems