Calape Bay is a semi-enclosed marine system located in Bohol, Central Philippines. Despite the relatively restricted water circulation and dispersion of particulate organic matter, mariculture activities have not decreased in Calape Bay. Organic matter (OM) content of the surface sediment was quantified to serve as indicator of the current status of the benthic system after almost 30 years since mariculture was launched. Surface sediments were mainly composed of sand and gravel. Highest sediment OM (15.3%) was observed at the middle portion of the bay where the mariculture facilities are located. Mean OM at the mariculture facilities (11.4%) was higher than at the mouth of the bay (5.7%) and near the river mouth (9.4%). Finer sediments contained more OM. The high sediment OM in the bay will bring changes in the benthic environment in the years to come if mariculture activities are not regulated. Hence, monitoring of sediment OM is recommended.