Wetland soils constitute vast, under-exploited and sometimes undiscovered ecologies in many countries of the World, including Nigeria. A total of 54 wetland soil samples including surface and subsurface soil at depths of 0-15 cm and 15-30 cm were collected using a sterile hand auger for a period of three months between August and October and subjected to standard and analytical microbiological procedures. The wetland soil samples were further subjected to atomic absorption spectroscopy (AAS) to check for presence and concentration of heavy metals. Results obtained showed that apart from heterotrophic bacterial and fungal counts, hydrocarbon utilizing bacteria (HUB) counts were higher in the surface soil ranging from 12.06±3.43bX107 cfu/g at Iwofe to 6.19±2.67aX107 cfu/g at Chokocho while subsurface soil had HUB ranging from 8.91±6.67aX103 cfu/g at Eagle Island to 4.93±3.95aX103cfu/g at Chokocho. Heavy metals such as Fe, Pb, Cd and Ni were recorded in concentrations above FEPA permissible limit in the surface and subsurface soil across the three wetlands. The heavy metal concentration in each wetland however, decreased with an increase in soil depth. According to literatures, elevated levels of heavy metals in soils decrease microbial population, diversity and activities. However, the microbial population in this study increased with increasing heavy metal concentration which indicates that the microbes can tolerate or utilize heavy metals in their systems; as such can be used for bioremediation of heavy metal polluted soils.