Coastal canal and waterway development has expanded rapidly over the past half-century, contributing to environmental issues such as declining water quality and saltwater intrusion. This study analysed 35 years of field sampling data from a subtropical meromictic lake to investigate water quality changes caused by intermittent saltwater intrusion. Saltwater intrusion began after a canal expansion converted a stormwater pipe into a bidirectional conduit, allowing saltwater to flow into the lake during high tides. Lake surface water temperature increased at a rate of 0.019 °C p.a. and pH has shifted from acidic to circumneutral over the study period, likely due to the disturbance of a pyrite layer during the initial construction phase and progressive increases in trophic state. Salinity accumulation in the bottom waters has caused the lake to transition from monomictic to meromictic, with stratification increasing through the 1990s, as evidenced by increases in Schmidt stability index. This shift to meromixis has resulted in permanent bottom-water deoxygenation and has led to eutrophication, evidenced by elevated nutrient levels and the development of a deep chlorophyll layer at the chemocline of the lake within recent years. This study provides valuable insights for managing other coastal lakes and wetlands experiencing similar challenges, offering guidance on mitigating the adverse impacts of saltwater intrusion that may increase with sea level rise due to climate change.