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Abstract This study evaluates the strategies to control microorganisms in the near wellbore area of water injection wells during secondary oil recovery. Biomass accumulation in the water injection wells can increase injection pressure and generate H2S. Nitrate injections can often overstimulate nitrate-reducer’s growth, increasing biofouling and souring downhole. Thus, control of microbes near wellbore must include the concomitant control of SRB activity and the reduction of the total microbial population. We evaluated strategies to reduce biofouling, increase injection flow and decrease H2S in simulated wellbore conditions. Sand-packed bioreactors containing soured biofilms were treated with different biocide formulations over 10 weeks. Volatile fatty acids, sulfide, and swept volume rates were used to evaluate the decrease in biofouling and microbial souring. Inlet and outlet biocide residuals were measured to determine loss of the chemistry during treatments. Genomic analysis (DNA Sequencing) was performed in fluids and core samples to determine shifts in the microbial population and to correlate the observed reduction in sulfide concentration and biofouling. The results showed that biocide shock treatments successfully mitigated the production of H2S in souring wellbore conditions and prevented rebounds and spikes of H2S between treatment cycles. Nonetheless, control of biofilms and biofouling was significantly more difficult to control under the same conditions, as the microbial populations quickly regrew after treatments, based on the increased consumption of volatile fatty acids after biocide treatment cessation. Biofouling and souring were not observed in control reactors that received biocide treatments since day one, highlighting the importance of a preventative approach to prevent chronic wellbore contamination. These results indicate that biofouling and H2S production are two phenomena that can be uncoupled as distinct problems during water injection. Additionally, our observations point to the importance of using different strategies to simultaneous control of souring and biofouling in near wellbore injection wells as a means to increase injectivity and sweet production. This paper will significantly expand the knowledge about water injection procedures and propose new strategies to control undesired microbial contamination in the near wellbore area. These strategies can help to prevent loss of production due to poor water injection and minimize the contamination of produced fluids by H2S gas.