This study assessed the levels and distribution of selected persistent organic pollutants (POPs) in water of River Niger. The selected POPs of interest were organochlorine pesticides (OCPs). Fifteen representative sites along River Niger: three each from Gurara River (tributary) in Niger State, Lokoja (confluence) in Kogi State, Onitsha in Anambra State, Brass and Nicolas Rivers (tributaries) in Bayelsa State were selected for sampling quarterly over a 24-month period. A total of 240 surface and bottom water samples were collected using Van Dorn water sampler in the eight quarters of 2008-2009. At the Delta locations where tidal effects take place, high- and low-tide water samples were taken as compared to surface and bottom at the River Niger locations. For sample extraction, EPA method 3510c was employed with slight modifications. Certified reference standards from Accustandards USA was used for the instrument calibration and quantification of OCPs. The extracted samples were subjected to gas chromatography (GC/ECD) for identification/quantification. And Shimadzu GCMS QP2010 was used for confirmation. Chlordane, endosulfan, endrin and DDT metabolites were very prominent in the water samples, compared to HCH, dieldrin, and isomers which occurred at lower concentrations. The sequence in the concentration of the organochlorine pesticides were ∑chlordane > ∑DDT > ∑endosulfan > ∑endrine > ∑dieldrin > ∑HCH. The highest concentration of ∑OCPs in water samples of River Niger, 1138.0 ± 246.7 ng/L, with range 560.8-1629 ng/L was detected at Onitsha location, while the lowest concentration, 292.6 ± 74.9, with range 181-443.0 ng/L was detected at Nicolas River. Levels of OCPs in a larger percentage of the samples exceeded guidelines and therefore hold potential harmful effects on benthic fauna, fish, and man. Abstraction of water from the River for drinking water treatment should be discouraged. Because of the potential danger, this presents, continuous monitoring of the water body and if possible remediation, determination of the sources of the POPs is therefore very necessary.