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Fecal coliform bacteria (FCB) contamination of natural waters is a serious public health issue. Therefore, understanding and anticipating the fate and transport of FCB are important for reducing the risk of contracting diseases. The objective of this study was to analyze he impacts of climate change on he fate and transport of FCB. We modified both the soil and the in-stream bacteria modules in the soil and water assessment tool (SWAT) model and verified the prediction accuracy of seasonal variability of FCB loads using observations. Forty bias correcting GCM-RCM projections were applied in the modified SWAT model to examine various future climate conditions at the end of this century (2076-2100). Lastly, we also compared the variability of FCB loads under current and future weather conditions using multi-model ensemble simulations (MMES). The modified SWAT model yielded a satisfactory performance with regard to the seasonal variability of FCB amounts in the soil and FCB loading to water bodies. The modified SWAT model presented substantial proliferation of FCB in the soil (30.1%-147.5%) due to an increase in temperature (25.1%,). Also, increase in precipitation (53.3%) led to an increase in FCB loads (96.0%-115.5%) from the soil to water body. In the in-stream environment, resuspension from the stream bed was the dominant process affecting the amount of FCB in stream. Therefore, the final FCB loads increased by 71.2% because of the growing peak channel velocity and volume of water used clue to an increase in precipitation. Based on the results of MMES, we concluded that the level of FCB would increase simultaneously in the soil as well as in stream by the end of this century. This study will aid in understanding the future variability of FCB loads as well as in preparing an effective management plan for FCB levels in natural waters. (C) 2018 Elsevier B.V. All rights reserved.