The final quarter of the year 2011, wide space flooding in Thailand was heavily affected to ecosystem in rivers. This research aims to compare water quality and benthic fauna diversity of the upper Chao Phraya River and the lower Ping and Nan Rivers in Nakhon Sawan Province between before and after the flood. The parameters including water temperature, turbidity, pH, conductivity, DO, BOD5, NO3 --N, NH3-N, PO4 3-, coliform bacteria and fecal coliform bacteria were measured. In the aftermath of flood situation, the results indicate that water quality of rivers after the flood is lower than before the flood but both of them not lower than the surface water quality standard. Comparison of the benthic fauna diversity in rivers shows the significantly change as a result from the flood. Data collect after the flood shows the decreasing of the diversity and the evenness of benthic fauna in sites affected by flooding.