This study investigates the diverse microbial communities in the polluted surface waters of Mar del Plata's port and surrounding areas, emphasizing their response to physicochemical parameters and pollutants. Minimal variations in temperature, pH and conductivity were observed. There was a predominance of organic matter quantities expressed in terms of Chemical (COD) and Biochemical Oxygen Demand (BOD) typical of water with recalcitrant organic matter. While bacterial communities were dominated by Proteobacteria, with notable Vibrio sp. and Alteromonadaceae populations, eukaryotic communities were rich in Diatomea and Dinoflagellata. Despite physicochemical variations, overall microbial community composition remained stable. Specific taxa, such as Alcanivorax sp. and Paraglaciecola sp., were exclusively found in the port and could serve as pollution indicators. This study enhances our understanding of microbial ecology in harbor marine environments and surrounding areas, providing essential data for ecological assessments and conservation efforts in Mar del Plata port and similar coastal regions.