Abstract Natural disasters have been entangled with life of human directly or indirectly. Flooding after heavy rainfall is one of the terrific and most common hazards which can have serious influences on human health by creating suitable environments to form water borne diseases. Leptospirosis is one of the major diseases caused by flooding in Sri Lanka. Thus, this study identifies the effects of floods especially on the spread of leptospirosis in Sri Lanka. Three distinct data sets were used for this study: the first was the records retrieved from Disaster Management Centre and Disaster Management Unit of Medirigiriya DS office regarding the retrospective rainfall and flooding incidents recorded during 2004-2016; the second was derived from the Regional Director Office of Health Service (RDHS) to recognize the number of leptospirosis cases recorded during the selected period; and the third data set was collected using a questionnaire survey administered to people affected by leptospirosis disease in Medirigiriya. A chi-square test was used for statistical analysis and Arc GIS 10.3 was used for map analysis. The study could identify a clear relationship between floods and leptospirosis outbreaks in Medirigiriya as majority of victims could be identified in areas subjected to floods during the past years. According to the risk map, Atambaoya, Tissapura, Viharagama, Medirigiriya and Diulankadawala Grama Niladgari divisions were identified as more vulnerable areas for the disease than the other areas. In addition to floods, muddy paddy farming and livestock rearing practices are also reasons for the spread of the disease among people. Farmers who engage in muddy paddy fields were identified as the most vulnerable group to leptospirosis as they use contaminated paddy water to wash their faces and hands, drink and fulfill sanitary requirements. Direct ways of exposure to flood water including walking through contaminated water, doing water sports without wearing protective costumes also let the bacteria to sketch human body.