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This review examines the substantial changes that have taken place in marine habitats and resources of the Gulf over the past decade. The habitats are especially interesting because of the naturally high levels of temperature and salinity stress they experience, which is important in a changing world climate. However, the extent of all natural habitats is changing and their condition deteriorating because of the rapid development of the region and, in some cases from severe, episodic warming episodes. Major impacts come from numerous industrial, infrastructure-based, and residential and tourism development activities, which together combine, synergistically in some cases, to cause the observed deterioration in most benthic habitats. Substantial sea bottom dredging for material and its deposition in shallow water to extend land or to form a basis for huge developments, directly removes large areas of shallow, productive habitat, though in some cases the most important effect is the accompanying sedimentation or changes to water flows and conditions. The large scale of the activities compared to the relatively shallow and small size of the water body is a particularly important issue. Important from the perspective of controlling damaging effects is the limited cross-border collaboration and even intra-country collaboration among government agencies and large projects. Along with the accumulative nature of impacts that occur, even where each project receives environmental assessment or attention, each is treated more or less alone, rarely in combination. However, their combination in such a small, biologically interacting sea exacerbates the overall deterioration. Very few similar areas exist which face such a high concentration of disturbance, and the prognosis for the Gulf continuing to provide abundant natural resources is poor.