A complex evaluation of antimicrobial activities of microalgae, including those relevant to wastewater treatment (WWT), in light of the integrated biorefinery concept, is performed. An example of this concept is linking a commercial microalgal system to plants, factories, or farms that emit polluted wastewater (WW). The microalgae would not only metabolize the pollutants—such as nitrogen (N) and phosphorus (P)—from the WW, thus fueling their biomass, but they would exert an antibacterial effect against the pathogenic bacteria there. The biomass then could be harvested and used for biofertilizers, biofuels, and bioplastics and might possibly be utilized as animal feed, antimicrobial and other pharmaceutical agents. A large amount of the research on the antimicrobial activity and WWT potential focuses on the families Chlorellaceae and Scenedesmaceae, which are also some of the most commercially used strains of microalgae. For that reason, they are the species chosen for the current review. Furthermore, the increasing antimicrobial resistance necessitates the search for antibiotic alternatives, and the antibacterial and antifungal activity of Chlorellaceae and Scenedesmaceae is very promising. Microalgae are rich in antibacterial compounds like polyunsaturated fatty acids (PUFAs), polysaccharides, carotenoids, proteins, etc., and for that reason, their extracts possess antimicrobial effects. The in vitro antimicrobial activity of Chlorellaceae and Scenedesmaceae families has varied in a broad range from low to strong activity or no effect. Several strains have fulfilled the criteria for outstanding and high activity, especially C. vulgaris and other Chlorellaceae spp., with an effect equal to or better than the control antibiotics. There were several strains with minimum inhibitory concentrations (MIC) below 80 µg/mL and even 10 and 1.5 µg/mL; some species also had inhibition zones (IZ) over 30 mm, even as high as 48 mm. In vivo results are also promising but scarce, and all this warrants further in vivo and in situ studies—from animal models to clinical and environmental trials. Altogether, important data in the light of the circle economy, the urgent necessity to decrease CO2 emissions to fight climate change, and to curb the harmful influence of future pandemics are presented. This review paves the way for further utilizing the total potential of a microalgal system.