Heavy metal (HM) pollution has become a serious threat to coastal aquatic ecosystems. This study, therefore, aimed at assessing the spatial distribution of selected heavy metals/metalloids including Arsenic (As), Cadmium (Cd), Chromium (Cr), Lead (Pb), and Mercury (Hg) in surface sediment (0–15 cm) samples collected across Kalametiya Lagoon in southern Sri Lanka. Forty-one (41) grid points of the lagoon were sampled and the sediment samples were analyzed for HM content by using ICP-MS. A questionnaire survey was carried out to investigate the possible sources for HM pollution in Kalametiya Lagoon. Water pH and salinity showed significant variation across the lagoon. Overall mean value of pH and salinity were 6.68 ± 0.17 and 2.9 ± 2.2 PSU respectively. The spatial distribution of the heavy metals was not monotonic and showed a highly spatial variation. The kernel density maps of the measured heavy metals demarcated several different areas of the lagoon. The mean contents of As, Cd, Cr, Hg, and Pb were lower than that of threshold effect level (TEL) however, higher for Hg at the North Inlet. Nevertheless, it was still lower than potential effect level (PEL). Socio-economic interactions have dramatically reduced during the past two decades. Industrial sewage, river suspended sediments and agrochemicals such as fertilizers, pesticides were reportedly identified as the possible sources for heavy metal loads. Accumulation of toxic heavy metals can be minimized by detouring the water inflow to the lagoon.