Heavy metal pollution has become a serious threat to coastal aquatic ecosystems. Therefore, this study, aimed to assess the spatial distribution of five selected heavy metals/metalloids, arsenic (As), cadmium (Cd), chromium (Cr), lead (Pb), and mercury (Hg), in surface sediment samples collected from the Kalametiya Lagoon in southern Sri Lanka. Sixteen (16) areas of the lagoon were sampled. The sediment samples were analysed for heavy metal content by using ICP-MS while the water samples were measured for salinity and pH. A questionnaire survey was conducted to investigate the possible sources of heavy metal pollution in the Lagoon. Water pH and salinity showed significant variations across the lagoon. The 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 monotonous and showed a high spatial variation. The kernel density maps of the measured heavy metals demarcated several spatially different patches in the lagoon. The mean levels of As, Cd, Cr, Hg, and Pb were lower than the threshold effect level (TEL) although it was higher for Hg in the North inlet. Nevertheless, it was still lower than the potential effect level (PEL). Industrial sewage, river suspended sediments, and agrochemicals such as fertilizers and pesticides were identified as the possible sources for heavy metal loads. Accumulation of toxic heavy metals can be minimized by bypassing the freshwater inflow to the lagoon.