The new millennium has witnessed increasing growth of piracy and other illicit activities along East Africa brown waterways, with national governments seeking to contain them, despite immense challenges. The paper uses case study descriptions of Lake Victoria and Congo River economies to outline how illicit brown-water activities (e.g., pirates, illicit traffickers, and warlords) impede wealth and progress in areas desperately needing both. In light of current trends, these examples serve as exemplars for the effect of illicit activities occurring in the Great Lakes Region (GLR). These examples support the argument that Tanzania, Uganda, and Kenya – countries bordering Lake Victoria, along with the DRC, which contains the Congo River (and possibly the Central African Republic, Zambia, and other river basin countries) – must pursue concerted action together and with other international partners, such as the United States, to address the problem of destabilizing, illicit activities in brown waters. Such efforts will help to strengthen the projection of central government influence while bolstering weak national economies. This paper addresses three main objectives: (1) identify and assess illicit trafficking and piracy activities in Lake Victoria and the Congo River; (2) examine the potential impact of these activities on the local economy and the local population; and (3) identify the potential intervention options by national and international partners.