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The benthic foraminifera are a single cell protist that are highly abundant in marine and marginal environments. They have been successfully used in many monitoring works to elucidate the status of environmental health conditions. The present study examines the foraminiferal distribution in the surface sediments of the Sungai Kilim, within the Kilim Geoforest Park, in Pulau Langkawi, Malaysia. Information provided by benthic foraminifera were associated with geochemical properties, sediment types, and current speed data to characterise the environment. Twenty-eight genera of benthic foraminifera were identified from the surface samples. Elphidium spp. (relative abundance of 13–83%) were the most abundant species in the mangrove and lagoon environments along the Sungai Kilim. Salinity, water depth, and temperature were the important parameters that determined the foraminiferal distribution. Test abnormalities were observed in Elphidium spp. (< 10% of tests) at several stations; a higher quantity of abnormal tests (5–6%) were observed at stations with high current speeds, especially in mangrove areas. The sediment in the study areas did not show severe heavy metal contamination; therefore, the low diversity and test abnormalities were associated with natural stress from environmental conditions. This information provides a baseline for future environmental monitoring to preserve the Sungai Kilim and the Kilim Geoforest Park.