A study to assess the impact of wastes from Onuimo (Imo Rescue Mission) market on the microbiology of Imo River was carried out. Sediment and water samples were collected monthly and analysed quantitatively for faecal bacteria indicators of pollution and qualitatively for specific pathogens. The study reveals that the sites were heavily polluted with faecal bacteria (90 – 205 cfu/100 ml TVC and 17 – 64 cfu/100 ml TFC in water sample, and 51 – 216 cfu/100 ml TVC and 6 – 140 cfu/100 ml TFC in sediments) that consistently exceeded the World Health Organisation (WHO) recommended range for potability. These organisms often comprised the pathogens; Shigella spp., Salmonella spp., Escherichia coli, Candida spp., Enterobacter aerogenes, and Staphylococcus spp., which seemed to be pervasive. They all tended to be highest in water samples during rainy season and in sediment samples during dry season. There is spatial variation (P>0.05) with point B as the most impaired segment. The findings show that the river is under heavy pollution due to wastes from the market and households around the river; and thus does not meet the World Health Organisation standards for domestic, irrigation and aquaculture purposes. The water should therefore be treated properly before use.