Top Lagoons in Sri Lanka: Hidden Waters Worth Exploring

Sri Lanka is famous for its beaches and wildlife-rich national parks, however beyond the well-trodden path is a less explored ecosystem – its lagoons. Scattered along the coastlines, these tranquil locations offer biodiversity, culture and adventure. From Negombo in the west to Batticaloa in the east, Galle in the south and Jaffna in the far north, these lagoons in Sri Lanka are perfect for nature lovers and curious travellers who want to discover something unique.

Galle’s Hidden Lagoon

While Galle is known for its scenic Fort and iconic hotels like Jetwing Lighthouse, the countryside is home to hidden gems like Koggala Lagoon. Just 15 minutes from the city, this expansive, calm lagoon is fed by the Koggala River and is connected to the sea by a narrow channel.

Fewer tourists venture inland from the beach resorts, so this is a great place to explore peacefully. Cinnamon plantations, bird islands and Buddhist hermitages can be seen on its many islets. The area is rich in biodiversity and local guides will point out water monitors, monkeys and cormorants. Book boat safaris to explore popular spots like Madol Duwa and Spice Island. Along the way, you can also visit the Kathaluwa temple and centuries old murals or join a cinnamon peeling demonstration with local farmers.

Negombo Lagoon

Just a short drive from Colombo and minutes from Bandaranaike International Airport, Negombo Lagoon is one of the best spots to experience Sri Lanka’s lagoon ecosystems. Though the town is famous for its fish markets and colonial heritage, the lagoon is relatively unexplored.

The calm, brackish waters stretch over 35 square kilometres and are fringed by mangroves, fishing villages and narrow canals. One of the best ways to experience the lagoon is by canoe or traditional catamaran. At dawn or dusk, the mirror-like surface reflects the skies and fishermen glide across the water casting their nets.

Activities to do include booking lagoon boat tours through mangrove forests, lagoon fishing and going birdwatching to see herons, egrets and kingfishers abound). Don’t miss visiting the beautiful Muthurajawela Wetland Sanctuary nearby for eco-tours. Visitors can book a stay in top hotels in the area such as Jetwing Blue, Jetwing Beach and Jetwing Sea.

Batticaloa Lagoon

On the other side of the coast, Batticaloa Lagoon stretches 50 kilometres, and is one of the largest lagoons in the country. Locally known as “Mattakkalappu”, it’s also home to a rare phenomenon, singing fish. On quiet nights, especially near the Kallady Bridge, locals say you can hear mysterious musical vibrations rising from the water.

Surrounded by fishing villages, Dutch-era forts and palm-fringed shores, Batticaloa’s eastern lagoon is a serene retreat with historical charm and natural beauty. You’ll also find prawn traps and fish farms dotting the shallows—evidence of its importance to the local economy.

Things to do here include going on lagoon boat tours near Kallady Bridge and Puliyanthivu Island and exploring the Batticaloa Fort and lighthouse. You could also relax at Pasikudah or Kalkudah beaches.

Jaffna’s Forgotten Lagoon

Less visited than the south, Jaffna is known for having almost unspoiled natural beauty. Among its gems is the Jaffna Lagoon, a vast shallow lake that stretches across the northern peninsula. Though it was closed off during the war, the region has opened up in recent years, and is a great spot for lagoon tourism.

The Jaffna Lagoon is a rich ecosystem, home to migratory birds, salt pans and rare marine life like sea cucumbers. With fishing huts and causeways around the lagoon, the area is stunning, and offers a glimpse into Tamil Sri Lankan culture.

Visitors can explore the salt flats and causeways around Elephant Pass or go birdwatching in the Chundikulam Sanctuary. Other options include Kayts or Karainagar islands via causeway, with views over the water.

Travellers to the North can find luxurious lodgings, such as the first luxury hotel in the city, Jetwing Jaffna.

Whether you’re an eco-tourist or photographer, Sri Lanka’s lagoons offer some of the most amazing nature experiences.