The effect of waste phosphogypsum obtained after phosphoric acid production from apatites and phosphorites, on the processes of denitrification and desulfurication taking place with the use of bacteria from the genera Bacillus and Desulfotomaculum, have been investigated. It has been shown that the phosphogypsum concentrations used in the experiments were can serve as a sulphate source for the Desulfotomaculum bacteria. The phosphogypsum is not toxic towards the bacteria. The phosphogypsum has also been found to play the role of an electron acceptor in the processes of oxidation of simple organic substrates in the processes of bioreduction of nitrates or sulphates. In the optimum conditions of desulfurication in a medium containing the phosphogypsum, organic substrate and Desulfotomaculum ruminis bacteria, the degree of conversion is close to 90%, and a decrease of TOC reaches about 50%.