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A baseline survey of macrobenthic fauna inhabiting shallow subtidal habitats was carried out around Huwar islands during two different cruises in May 2003. A total of 144 quadrats (0.25 m2), 48 subsurface seawater samples and replicate samples of sediments from 16 sites resulted in a collection of 119 species belonging to macrobenthos. Physicochemical parameters of the seawater namely depth (0.2 - 1.5 m), water temperature (28-32°C), pH (7.5-8.0), and dissolved oxygen (5.7-8.5 mg l-1) did not vary significantly between eastern and western shores. However, marked variation in salinity (46.5-54.5 ‰) and chlorophyll-a content of seawater (0.58-6.3 μ g l-1) were found. There was some indication that the eastern coast is more biologically diverse. Sediment organic content was slightly higher along the eastern coast. The substrate was typical of other areas around Bahrain and composed of sand, mud and harder encrustations. Grain size analysis indicated the dominance of fine to very fine sand fractions. Microbial indicators of seawater contamination were found in five of the sixteen sites and Enterococci were found at almost all sites with higher numbers recorded along the western coast. Similar results were found for Salmonella-Shigella counts. The total coliform count was over 100 Colony Forming Units with the exception of a few sites, and a considerable total vibrio count was also recorded. The island's coastal water was nevertheless considered relatively clean from pathogenic bacteria as compared to other areas around Bahrain. A monitoring of macrobenthos and pathogenic bacteria should be conducted in order to endure good water quality around Huwar. A survey of this sort requires dedicated time and resources in order to establish a monitoring program because of the fast rate in urban developments within this region. [ABSTRACT FROM AUTHOR]