Microorganisms are a nuisance in water injection systems. Dense bacterial growth within the pipelines is the originator of reservoir souring, biofouling, biocorrosion and biodegradation of the infrastructure, resulting in huge expenses on the operational and capital costs. Molecular methods are superior tools for identifying microbial populations in the system and mapping the threat level. qPCR is a technology that allows us to quantify the absolute concentration of different bacterial and archaeal groups present in samples collected in the field. This analysis can be done on-site or in-laboratory. Another technology called next-generation sequencing (NGS), can dig deep into the interesting samples to determine the identity and relative populations of specific bacteria and archaea down to the genus or species level that are present. However, both of these techniques cannot differentiate between viable and non-viable communities. Recently RNA based estimations have been observed as a method to quantify the living microbial communities. Coupling RT-PCR, qPCR and NGS together gives a complete picture of what is happening and thus opens avenues for more effective monitoring and treatment.