Freshwater is a scarce resource and faces significant issues with chemical pollution. Antibiotics and heavy metals are some of the chief contaminants found in freshwater. Developing efficient technologies to treat freshwater is becoming increasingly important. Bioremediation is an environmentally friendly and efficient technology that can be used in this regard. In this process, contaminants like antibiotics and metals are degraded or eliminated by molecular mechanisms of the microorganism such as enzymatic oxidation, enzymatic reduction, biosorption, bioaccumulation, precipitation, and the formation of biofilms. Microorganisms play important roles in bioremediation. For example, microbial genera such as Bacillus, Rhizopus, Klebsiella, Enterobacter, Alcaligenes, Pseudomonas, and Brevibacterium are among the top candidates for metal bioremediation. Similarly, bacterial genera such as Microbacterium, Burkholderia, Stenotrophomonas, Acinetobacter, Escherichia, and Bacillus along with microalgae, mixed algae-bacteria consortiums, and fungi are effective at antibiotic bioremediation. This review discusses general concepts of bioremediation followed by the roles and examples of microorganisms in metal and antibiotic bioremediation. Bioremediation has the potential to become an environment-friendly technology to reduce surface water pollution. This review also discusses investigations related to molecular mechanisms of bioremediation. Understanding these mechanisms can unfold the processes behind microbial bioremediation and guide the design of efforts to remove contaminants like antibiotics or metals from wastewater in the future.