Biofilms are assemblages of single or multiple populations that are attached to abiotic or biotic surfaces through extracellular polymeric substances. Gene expression in biofilm cells differs from planktonic stage expression and these differentially expressed genes regulate biofilm formation and development. Biofilm systems are especially suitable for the treatment of recalcitrant compounds because of their high microbial biomass and ability to immobilize compounds. Bioremediation is also facilitated by enhanced gene transfer among biofilm organisms and by the increased bioavailability of pollutants for degradation as a result of bacterial chemotaxis. Strategies for improving bioremediation efficiency include genetic engineering to improve strains and chemotactic ability, the use of mixed population biofilms and optimization of physico-chemical conditions. Here, we review the formation and regulation of biofilms, the importance of gene transfer and discuss applications of biofilm-mediated bioremediation processes.