The aim of this study wa s to have a better understanding about the impact of flood to the ecosystem such as types of pollution and water quality level of rivers in Kelantan. This stud y wa s specifically carried out in a flooding prone area determine water quality level by using Water Quality Index (WQI) and Macrobenthos analysis to reach the objective of the experiment. In this study, samples from two major rivers in Gua Musang, Kelanta n were chosen to be analyzed as they were just hit by a major flood recently, those two rivers are Sg. Nenggiri and Sg. Lebir. Samples from these two rivers were analyzed using Water Quality Index (WQI) and Macrobenthos analysis method so that a comparison can be carried out between the two methods and to identify the distribution of benthic invertebrate in the fau na. Results from the analysis were then compared to the water quality index before the flooding event given by Department of Environment (DOE). T his study h as achieved its objective by thorough and carefully analyzed results where the WQI and BWQI value were obtained and compared. WQI value for Tributary Sg. Nenggiri wa s 78.06 classified into class II with a slightly polluted river status while the BWQI value for this river wa s 6.07 also categorized into class II with rather clean status. Sg. Nenggiri and Sg. Relai on the other hand has a WQI value of 90.31 and 85.01, both are classified into class II with a clean river status while the BWQI shows a value of 6.63 and 6 with a rather clean status and belongs into class II. Sg. Paloh recorded a WQI value of 79.81, categorized into class II with a slightly polluted river status whereas the BWQI value for this river wa s 6.17 classified into class II with a rather clean status. From the comparisons made on WQI and BWQI we c an deduce that both method showed a similar result with a slight indifference that did not affect the accuracy of the results