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The coastal shelf of the Gulf of Oman experiences periodic upwelling events during the summer months that are driven by the southwest monsoon. It is unclear what role these events play in the spatial and temporal distribution of the region’s fish assemblage. We carried out trials on two different video techniques to characterize the habitat and fish assemblage along the continental shelf margin near Muscat, Oman. Exploratory surveys with a drift stereo-video revealed three main habitat types: Sand, Reef and Megabenthos. Three areas were chosen for additional sampling using stereo-BRUVS (‘baited’ remote underwater-video systems). On two separate occasions (November 2005 and March 2006) replicate stereo-BRUVS were deployed in each area stratified by the main habitat types. For each teleost and elasmobranch species encountered on the video, an estimate of total body length and the relative abundance (MaxNi) was made. The stereo-BRUVS recorded a wide range of demersal and pelagic teleosts including species of conservation interest such as sharks, rays and groupers. The drift stereo-video recorded significantly fewer species than the stereo-BRUVS (N = 15 versus N = 43). Species diversity from the stereo-BRUVS increased by 96% in March 2006 (N = 41) compared to November 2005 (N = 23), a pattern consistent at all three areas. The structure of the overall fish assemblage (using canonical analysis of principal coordinates analysis) was highly variable both in time and space. There was ample evidence of strong habitat associations, particularly with depth and seasonal shifts in abundance and diversity. We argue the upward migration of oxygen-depleted water into the shallow depths during the late monsoon displaces the demersal fish community along this coast.