Coral reefs and other sensitive marine habitats around Kayankerni are threatened by a number of human and natural impacts. Although direct human impacts are relatively lower than in many other areas of Sri Lanka managing existing threats now is critical for the long term conservation of Kayankerni Marine Sanctuary.
Export driven fisheries for groupers, snappers, parrotfish and other reef fish can have impacts on the populations of these species. Some fishing methods can also cause damage to coral reefs. Primarily among them are bottom set nets that result in the entanglement and damage of corals. Although not practised within the MPA illegal fishing using explosives is a major problem outside the MPA and can have major impacts on fish populations and habitats.
Accidental bycatch of species such as turtles in fishing nets is of concern, while turtle nests are also under threat from domestic dogs. The growth of aquaculture in the surrounding area can have indirect impacts through the release of effluents that contain high levels of nutrient, other pollutants and pathogens into waterways that eventually reach the sea. Similarly high rates of sediment and nutrients from agriculture in the Maduru Oya basin is eventually released into coastal waters via the Valachchenai estuary. This can lead to increased algal growth, spread of disease and loss of coral cover.
In addition there are several major natural threats to coral reefs in the area. Coral bleaching due to increased sea temperatures is a major concern for coral reefs around the world. Coral bleaching has been recorded in Kayankerni every year from 2015 - 2019 with major bleaching events in 2016 and 2019. Although coral mortality was relatively low in 2016 there was significant coral mortality in 2019 resulting in some sections of the reef losing more than 90% of live coral cover. Other natural impacts include invasive species such as the coral eating Crown of Thorns starfish and the spread of algae such as Halimeda and Caulerpa possibly linked to changes in water quality.