A study was conducted to evaluate the concentration of heavy metals, and the physicochemical and microbiological properties of wetland soils at the University of Lagos. Soil samples were randomly collected from the Faculty of Science (FSC), Lagoon Front, and Distance Learning Institute areas at depths of 5 cm, 10 cm, 15 cm, and 20 cm using a soil auger. The samples were stored in sterile nylon bags, appropriately labelled, and transported to the University of Lagos Central Research Laboratory for chemical analysis. The physicochemical characteristics measured included soil pH, determined using a pH meter, and moisture content, assessed through the oven-drying method. Heavy metal concentrations were analyzed using an Atomic Absorption Spectrophotometer. Microbial population diversity was examined using the disc diffusion method. Statistical analysis was performed using SPSS version 20, and mean values were evaluated using Tukey’s multiple comparison test at a probability level of P < 0.05. The results revealed that soil pH ranged from 7.20 to 8.81, with the highest value (8.81) recorded near the Faculty of Science (FSC-3). Eight heavy metals, including Pb, Ni, Cr, Cd, Fe, Cu, Mn, and Zn, were analyzed. Lead concentrations ranged from 0.02 to 0.29 ppm, followed by nickel, which ranged from 0.01 to 0.13 ppm. Chromium ranged from 0.0 to 0.25 ppm, cadmium from 0.03 to 0.08 ppm, iron from 1.02 to 2.96 ppm, copper from 3.31 to 4.60 ppm, manganese from 3.31 to 5.16 ppm, and zinc from 1.67 to 9.17 ppm. Lead and zinc concentrations were found to be below the permissible limit at all locations, while chromium and cadmium were within permissible limits. However, Zn, Mn, Cu, Fe, and Ni exceeded the permissible limits. Correlation analysis revealed a significant correlation (P < 0.05) between Pb and Zn, likely due to effluents from human waste and seepage from nearby dumpsites into the lagoon, streams, or beaches. The isolated microbial flora included three bacterial genera, Bacillus megaterium, Bacillus spp, and Enterobacter spp, as well as four fungal genera, Aspergillus, Penicillium, Aspergillus flavus, and Fusarium. Bacterial counts were lower than fungal counts in polluted soils, likely due to the nutrient status of the soil. The isolates were found to be tolerant to slightly alkaline pH and heavy metal pollutants, with microbial variation attributed to the impact of pH and heavy metals on the microbial population.