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The survival of dolphins and dugongs in the waters of Tanzania faces multiple challenges. These include incidental and directed catches and loss of or degraded habitat. As of 1998, few major studies have been made of the status and abundance of marine mammals in Eastern Africa.

Deforestation rapidly affects ecosystems. Heavily logged areas were compared with unlogged areas using spatial variations in benthic macrofauna and nutrient dynamics at locations in Tanzania. The areas showed significant differences in nutrient content, specifically for nitrate, ammonia and phosphate levels. The logging rate at the heavily logged site is not sustainable.

Dynamite fishing seems to have significantly damaged a coral reef in Tanzania. The Taa reef was severely damaged, and research has shown coral larvae usually settled on lower surfaces while dynamite fishing has removed viable seed populations for corals. Other factors affecting restoration of this habitat included sedimentation rates and competition for space with other species.

Sustainable coral reef management is a crucial issue for people living near the coast of Zanzibar. The coral reefs of these islands are extensive, and have been actively used as resources for centuries, but increasing population pressure has created greater demand as well as greater exposure to pollution and physically destructive activities. Overexploitation, fishing and anchor damage, and pollution are the principal challenges Zanzibar coral reefs face.

Prawn farming is a growing industry in Sri Lanka, yet it is threatened by water pollution related to agriculture. Land-based farming was found to place unusually high levels of aluminum, manganese, and iron. This produced poor shrimp quality, high incidence of disease symptoms, socioeconomic problems and growth retardation. Improved planning that accepts socioeconomic factors in locating shrimp farms could help improve the industry's sustainability.

The Western Indian Ocean Marine Science Association (WIOMSA) promotes the educational, technological, and scientific development of all marine sciences throughout this region. Inaugurated in Dec 1991, this nonprofit organization permits its members a place to communicate and exchange information, and has formed partnerships with other international and regional organizations. WIOMSA has strong potential for growth, with a need for a stronger financial base.