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The comparative assessment of two rivers, Warri River (Delta State) and Ule River (Edo State), in the Niger Delta region of Southern Nigeria was carried out between the months of January and June, 2016 across wet and dry seasons using two pollution indices of water quality index (WQI) and physical pollution index (PPI). Results from this study when compared with existing standards revealed the pollution state of the two rivers as occasioned by anthropogenic activities and flooding from the surrounding watershed. While WQI values for Warri River ranged from 440.9071-1077.9974 for station 1 and 4222.3909-1067.7317 for station 2, WQI values for Ule River ranged from 175.1432-482.4832 and 199.1039-416.4238 for stations 1 and 2 respectively. The PPI values of Warri River ranged from 27.919-99.030 for station 1 and 29.851-82.284 for station 2 while PPI values for Ule River ranged from 6.491-10.632 for station 1 and 6.829-11.381 for station 2. Warri River recorded the highest mean WQI of 714.9793±125.7361 for station 1 and 704.5335±105.198 for station 2and highest mean PPI values of 67.455±12.364 for station 1 and 57.633±9.602 for station 2compared to Ule River with lower mean WQI values of 316.045±49.076 for station 1 and 294.795±32.837 for station 2 and lower mean PPI values of 7.998±0.734 for station 1 and 8.367±0.940 for station 2 respectively. The wet season has more influence on the quality of both water bodies. The findings of this investigation reveal that the water is not fit for drinking and other domestic purposes.This is a signal to the Government and Environmental Protection Agencies (EPA)to promulgate laws restricting industries and individuals from dumping waste materials into the water bodies. Proper means of waste disposal in the environment should also be developed so as to conserve and preserve the aquatic ecosystems.