Abstarct: Flood, is one of natural disasters, causes considerable dameges annually in almost all parts of the world including Iran. Qamsar and Ghohrood basins are located in south of Kashan include occasionally flood happening. There is no comprehensive study on flood characteristics in Qamsar and Ghohrood so far. There for the main aim if this research is assessing the potential of flooding in the study region. In order to assess the flooding condition in the study region, after field abservation, the factors affecting runoff (including unconsolidated materials, slope, rainfall, vegetation and lithology) were identified. Then the laxyers of information related to the mentioned parameters prepared and weighted in the GIS environment and using expertness and AHP methods. After combining the above mentioned in formation laxyers the final map of flooding hazards was prepared. The obtained results indicate that the highest risk of flooding are located in south parts (upstream) of the basins. Moreover, using hydrometric data for the period of 1347-1392 the recharge coefficient was calculated for basins Qamsar and Ghohrood. In addition, the runoff coefficient has been calculated for seasons of winter, spring and summer in the study basins which equals 0.03, 0.02 and 0.26, respectively. Furthermore, Smada and Easyfit softwares have been used for determining the statistical distribution function and return period. The best statistical distribution for hydrometric data was Log Pearson type III distribution. Assessment of surface water quality in the studied basins indicates that the values of electrical conductivity and major ions have markedly increased for upstream to downstream in both basins.