The United Nations aimed to provide safe drinking water, sanitation, and hygiene (WASH) around the world, but flooding in Kota Tinggi, Johor, Malaysia, may cause the country to miss its population coverage target of 92–97% by 2030. Due to limited access to clean water and sanitation, Kota Tinggi's rural communities faced significant WASH challenges, resulting in the spread of waterborne diseases. Meanwhile, worsening flooding in Kota Tinggi's town area may cause damage to WASH infrastructure, disrupting clean water and sanitation services in urban areas. The study sought to compare WASH provision in rural and urban areas, as well as to identify knowledge, attitudes, and behaviours concerning flooding, flood prevention, and water-related infectious diseases. We surveyed 30 and 50 households from rural and urban areas in Kota Tinggi respectively. The findings revealed that both communities practiced safe drinking water, but at varying levels of sanitation facility availability, with urban areas proving to be more prosperous than rural areas. There was a significant difference in flood knowledge and perceived flood risk between rural and urban communities, resulting in different levels of flood preparedness. To summarize, improving WASH provision and flood preparedness in Kota Tinggi requires a tailored approach that addresses the specific needs of both rural and urban communities.