The Arabian Gulf is increasingly subjected to habitat alteration due to dredging, reclamation activities, and pollution from various anthropogenic sources, including industrial and domestic effluents and oil spills. These activities can affect the naturally stressed marine ecosystems. Genotoxicity and cytotoxicity biomarkers are widely recognized as an important tool to assess the biological response of organisms exposed to a variety of contaminants. This study investigated the genotoxic and cytotoxic effects in bivalves influenced by marine pollution in Bahrain. The results revealed that high percentage of abnormal cells (45.57%) was associated with a shallow bay influenced by elevated levels of nutrients from a major sewage station. Characterization of genotoxic and cytotoxic biomarkers can be adopted to monitor coastal and marine areas influenced by anthropogenic land-based activities in the Arabian Gulf. © 2019 – IOS Press and the authors. All rights reserved.