Jaffna lagoon is a large lagoon off Jaffna District and Kilinochchi District, northern Sri Lanka.
The lagoon is surrounded by the densely populated Jaffna peninsula containing palmyra palms, coconut plantations, and rice paddies. There are numerous fishing villages and some salt pans.
The lagoon has extensive mudflats, sea grass beds and some mangroves. The lagoon attracts a wide variety of water birds including American Flamingoes, ducks, gulls, terns and other shorebirds.