The aim of this study is to assess flood risk zoning for the water supply system of Kashan City, including the wells, storage tanks, and transmission and distribution pipelines. To this end, the sub-catchments affecting the water supply system were first identified, and the runoff from each sub-catchment was calculated using the SCS rainfall-runoff model. By inputting the characteristics of the runoff hydrograph of each sub-catchment, two-dimensional hydraulic modeling was conducted in the identified waterways using HEC-RAS 2D software, and the flow characteristics, including depth and velocity, were calculated for a flood with 50-year return period. Subsequently, the flood hazard index was determined for the flood-prone components of the system. On the other hand, the vulnerability index of the components of the water supply system was determined using five indicators: extent and area of influence, possibility of replacement, possibility of reconstruction or repair, relative economic value, and degree of dependency. Subsequently, the flood risk for each component of the water supply system was calculated using the hazard and vulnerability indices, and a risk zone map was created for each component. The results showed that in the water supply system of Kashan City, there are 22 wells with a risk index ranging from 61.8 to 120.6, 7 storage tanks with a risk index ranging from 66 to 126, and 31 kilometers of transmission and distribution pipelines, including the Zayandeh Rud water transfer line, with a risk index ranging from 11 to 102 at flood risk. By identifying the higher-risk components, priorities were established for implementation to reduce flood risk, and solutions were proposed to mitigate vulnerability, decrease flood hazards, and ultimately reduce the risks associated with the components of the Kashan city water supply system.