This study’s aim was to evaluate the effect of prolong flooding on groundwater (borehole) qualities of selected communities of Southern Ijaw and Yenagoa LGAs in Bayelsa State Nigria. Sampling boreholes as groundwater in these communities, this study showed no difference in the pH of the groundwater for flood affected communities in Ogboloma, Okolobiri and Olodiama as against control pH (unaffected flood community) at Yenagoa. Electrical conductivity and TDS values of the groundwater for flood affected communities were below the control groundwater sampled. On the other hand, groundwater SO4 level of the flood affected communities ranged from 2 mg/l to 4 mg/l while SO4 value was not detected for the control groundwater at Yenagoa. Furthermore, groundwater NO3 and PO4 level for flood affected communities were lower than that of the control groundwater at Yenagoa. Iron (Fe), Chromium (Cr) and Lead (Pb) from the groundwater of flood affected and unaffected communities were all below 0.001mg/l. However, Copper (Cu) level from groundwater of flood affected communities were slightly higher than control groundwater at Yenagoa. The most significant effect of prolong flooding showed faecal coliform from the flood affected communities ranged from 1,100MPN/100ml to 2400 MPN/100ml while that of the control groundwater showed 7 MPN/100ml suggesting that prolong flood water may have eroded faecal matter into the groundwater of affected communities by 157 to 342 times