Crude oil exploration has been beneficial to our economy but detrimental to our environment with the artisanal refineries further compounding the challenge. This research was aimed at investigating the microbiology and heavy metal pollution of three crude oil polluted rivers in Rivers State, Nigeria and effects on living organisms inhabiting that environment. This study was carried out in three locations in South-South Nigeria (Eagle Island, Iwofe and Chokocho rivers). A total of 64 water samples (upstream and downstream points) were collected using appropriate containers and sterile polyethene bags for 6 crab samples for a period of three months. Water and crab samples were analyzed for heavy metals using Atomic Absorption Spectrophotometric method while microbiological analysis involved isolation and enumeration of microbial populations of the water and crab samples as well as characterization and identification of the isolates using standard methods Results showed Total Heterotrophic bacteria (THB) ranged from 6.0 × 106 cfu/ml to 9.0 × 108cfu/ml for the downstream locations and 1.7 × 106cfu/ml to 3.5 × 107cfu/ml for the upstream locations. Total Heterotrophic Fungi (THF) ranged from 2.0 × 104cfu/ml to 1.1 × 105cfu/ml for downstream locations and 0.1 × 104cfu/ml to 4.0 × 104cfu/ml for upstream locations, Hydrocarbon Utilizing Bacteria (HUB) ranged from 0.8 × 103cfu/ml to 4.0 × 103cfu/ml in downstream locations and 2.0 × 103cfu/ml to 7.4 × 103cfu/ml in upstream locations, Hydrocarbon Utilizing Fungi (HUF) ranged from 1.0 × 103cfu/ml to 6.0 × 103cfu/ml for downstream locations and 5.0 × 102cfu/ml to 8.0 × 103cfu/ml for upstream locations. The bacteria identified biochemically included Serratia sp., Enterobacter sp. and Salmonella sp. for the crab samples and Bacillus sp. was dominant in the water samples (Bacillus subtilis, Bacillus cereus, Bacilluscarboniphilus). The heavy metals (Fe, Ni, Zn, Cd, Cu, Mn, Cr and Pb) were below the DPR permissible limit but are likely to increase since the activities leading to pollution are still ongoing. The crab as a filter feeder, had higher concentration of heavy metals and microbial population and the location with the highest crude oil pollution (14.5mg/l) had the lowest THB (6.0 × 106cfu/ml) as physicochemical parameters like the amount of Dissolved Oxygen had been altered.