Gökçeada Salt Lake (GSL) (Gökçeada Island, North Aegean Sea) is an important wetland area situated on established bird migratory routes. The waterbody is subject to significant variability in seasonal water quality and species diversity. Monthly observations indicate that a total of 29 waterbird species were present during 2015–2016. Rainfall was observed to influence waterbird abundance. There was also a strong correlation between waterbird and zooplankton species diversity, with water quality a further influencing factor. The seasonal abundance of 78 other aquatic species was also investigated. Spring and fall seasonal eutrophication, as a consequence of canal construction and suspected warming due to climate change has caused changes in Chlorophyll-a, dissolved oxygen, biological oxygen demand levels and grazing habits of aquatic species. Here, we propose GSL as a coastal lagoon model for a hydrodynamically sensitive habitat undergoing significant change from the combined threats of heavy metal pollution from a waste management facility, pesticide use for tourism and agriculture activity and wider climate impacts. We conclude that our results provide a paradigm for broad-scale monitoring programs encompassing all components of the wetland ecosystem under anthropogenic and climate change pressure, thus providing a tool to support and inform essential management and rehabilitation plans.