It is expected that biotechnology plays a central role in making and keeping the environment clean. Most biological agents used for this purpose are microorganisms. A variety of cellular functions of microorganisms are potentially applicable to pollution prevention. These include dissimilatory oxidation and reduction of inorganic compounds, photosynthesis, co-metabolism of xenobiotics, biopolymer formation, and enzymatic transformation of heavy metals. The potential for using biological agents will be far greater if their abilities are enhanced by increasing the dosage of key genes and modifying their genetic regulation. The present review describes current efforts directed towards the genetic improvement of bacterial abilities to remove phosphorus and nitrogen compounds that are priority targets for controlling the eutrophication in natural bodies of water.