Microbial mats occur in nature as stratified communities of cyanobacteria and bacteria, but they can be cultured on large-scale and manipulated for a variety of functions. They are complex systems, but require few external inputs. The functional uses of mats broadly cover the areas of aquaculture and bioremediation. Preliminary research also points to promising uses in agriculture and energy production. Regarding aquaculture, mats were shown to produce protein, via nitrogen fixation, and were capable of supplying nutrition to tilapia (Oreochromis niloticus). Current research is examining the role of mats in the nitrification of nutrient-enriched effluents from aquaculture. Most research has addressed bioremediation, within which two majors categories of contaminants were examined: metals and radionuclides, and organic contaminants. Mats sequester or precipitate metals/radionuclides by surface absorption or by conditioning the surrounding chemical environment, thus bioconcentrating the metal/radionuclide in a small volume. Organic contaminants are degraded and may be completely mineralized. For agriculture mats hold promise as a soil amendment and nitrogen fertilizer. The use of mats in biohydrogen production has been verified, but is in a preliminary phase of development. We propose a comprehensive closed system based on microbial mats for aquaculture and waste management. (C) 2004 Elsevier Ltd. All rights reserved.