Biological treatment of environmental pollutants is often very complex and requires intensive control of operation parameters. Fermentation of microorganisms able to degrade or destroy pollutants is a key technology to ensure appropriate cell concentration and populations are maintained in the treatment system. Optimal operation strategies, especially policy for substrates feeding and oxygen supply, need to be developed to enhance the rates of biodegradation or biotransformation for efficient cleanup of the target pollutants. In this chapter, two unique types of biological treatment processes, namely, mercury detoxification and azo-dye decolorization, are introduced as the example to show how fermentation technology and bioreactor approaches are used to develop bioprocesses for environmental applications. Detoxification of mercury is conducted aerobically using wild--type and recombinant strains as the biocatalyst. The performance and stability of fed-batch and chemostat bioreactors for mercury detoxification are greatly correlated to the dosage of the toxic mercury substrate. In contrast, azo dye is less toxic but decolorization of azo dyes requires aerobic/anaerobic sequential environments. Thus, bioreactor design for bacterial decolorization focused on strategies for the supply of oxygen and retention of high cell concentration within the reactors to achieve optimal combinantion of aerobic cell growth and anaerobic decolorization. The effectiveness and feasibility of various bioreactor configurations and strategies are assessed.