Earth has limited resources that humans may exploit, even if it is mostly covered by water. Furthermore, most of these constrained resources act as routes for the discharge of household and industrial waste. Water bodies that receive effluents exhibit significant changes in their biological life forms as well as their chemical and physical attributes. It is believed that anthropogenic activities, which contribute to population growth, are the main causes of the significant rise in effluents that ultimately cause changes in the dynamics of water bodies. It goes without saying that despite significant advancements in waste water treatment techniques, effluents still include a variety of organic and inorganic, hazardous and non-toxic substances, as well as microbial bioburden. Microbial populations can undergo both qualitative and quantitative changes as a result of effluent discharge and the resulting physical and chemical disturbances. Furthermore, the microbial populations in the receiving water bodies exhibit even greater variability as the effluent fluctuates in quantity and quality. Alterations in the composition of microbial communities can cause hazard to the environment because they can lead to the emergence of more drug- and pollution-resistant species. Knowing how the microbial population reacts to exposed effluents becomes crucial in light of these considerations. While uncultivable bacteria continue to be a worry for these objectives, approaches such as metagenomics and genome sequencing might be investigated. Designing techniques that address both the maintenance of native microbial populations in water bodies and wastewater control is crucial. As a result, the present chapter summarizes how various effluents alter microbial populations and how such changes may affect the ecosystem.