The development of sustainable methods directed towards the synthesis of molecules is due to the heightened awareness and recognition of alternative eco-friendly and economical protocols that have minimum impact on environment. Among others, microwave (MW)-assisted methodology has matured and can be used safely to substitute for conventional laboratory heating techniques; a number of chemical transformations have been achieved thereby improving many existing protocols with superior results when compared to reactions performed under conventional heating conditions. The focus of this review is to summarize recent MW-assisted catalytic reactions performed in aqueous media for the development of environmentally benign protocols. We review the catalytic MW-assisted methods employed for the synthesis of a variety of heterocycles, cross-coupling reactions, C-H activation reactions, synthesis of peptides, ureas, and carboxyl-containing coordination polymers and a host of miscellaneous reactions. In addition, some recent newer developments such as continuous flow capillary MW microreactors and other related flow applications are included. This sustainable approach represents the fusion of friendly reaction medium (water) and microwave activation in conjunction with a variety of catalysts.