Uncontrolled microbial growth in oil and gas reservoirs may lead to microbiologically influenced formation damage (MIFD) including but not limited to (i) reservoir souring due to H2S production which can also cause health issues and downstream pipeline and equipment corrosion and (ii) reservoir permeability decrease due to clogging with biofilm. In this paper we present results from studies which illustrate the negative impact of biofouling in laboratory-scale porous media bioreactors and the impact of biocide treatments on the prevention and mitigation of the effects of MIFD. Porous media bioreactors without biocide treatment were found to develop high levels of planktonic bacterial growth and biofilm buildup with concurrent generation of H2S and deposition of iron sulfide. Biomass plugging of the porous media resulted in decreased permeability as measured by an increase in backflow pressure and flow interruption. In comparison bioreactors which received biocide treatments exhibited good or extended bacterial control had no or low biofilm growth and maintained higher permeability as compared to untreated controls. In addition to biofouling prevention it was also found that porous media systems with biofilm plugging could be remediated via biocide treatment with reduction of bacterial growth and backflow pressure after treatment. These experimental results in porous media bioreactor systems indicate that microbial control within the reservoir is essential to maintaining high injectivity and productivity for the duration of the well lifetime.