This baseline study investigates the benthic habitats of Kep, Kampot, and Koh Seh, filling knowledge gaps on the diversity and distribution of seagrass meadows, coral reefs, and bivalve beds.The region lacks reliable historical data, complicating monitoring and conservation efforts. The results serve as a benchmark for evaluating the efficacy of protected area delineation and anti-trawling structures as conservation measures. Species, density, percent coverage, depth, and substrate, were recorded via free-diving from 2022-2023. A grid survey was conducted at 250m intervals covering 71,985ha. A total of 11,569ha of seagrass, 2,688ha of bivalves, and 1,063ha of coral were observed, with the Kep MFMA hosting the highest habitat coverage. These data show a 39% decline in seagrass coverage in Kampot over the last ten years – there is no available data to calculate changes in benthic habitats in the other 3 survey zones. This serves as a crucial point of reference for successive studies on the region's ecological welfare and will help to estimate the value of current conservation methods.