Maduganga is located in the southwestern region of Sri Lanka where the southwestern group of crystalline rocks, which is one of the upper Paleozoic rock formations, predominates. Bog and half bog soils dominate this area. A total of 15 islands within the estuary are surrounded by water throughout the year, with Ma Duwa, Mirala Duwa and Dik Duwa forming the large islands. The Maduganga basin is situated in the wet zone of the country which experiences high rainfall during the northwest monsoon (average rainfall is 2,217 mm annually and subject to flooding). The mean monthly temperature is on average 27.20C. Maduganga is generally shallow, with a maximum depth of 2.5 m in most places (the deepest point is 3 m and the shallowest is 1.25 m). Tidal influence is small with a maximum of 10 cm. The temperature of the surface water is within the range of 30.1-33.70C. The pH range in Maduganga is between 6.95 and 8.98. The level of salinity depends on the tides, inflow of freshwater via different streams and whether the lagoon mouth is open or closed. Near the mouth of the estuary, the salinity levels vary between 6.7 – 20.8 ppt and gradually decrease with distance from the mouth. The estuary is connected to the sea by a narrow canal and the mouth of the estuary is often blocked by a naturally formed sand bar. It receives water from three major streams; Boralessa Ela, Heen Ela and Magala Ela.
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