Change in climate and water cycle will challenge water availability but it will also increase the exposure to unsafe water. Floods, droughts, heavy storms, changes in rain pattern, increase of temperature and sea level, they all show an increasing trend worldwide and will affect biological, physical and chemical components of water through different paths thus enhancing the risk of waterborne diseases. This paper is intended, through reviewing the available literature, to highlight environmental changes and critical situations caused by floods, drought and warmer temperature that will lead to an increase of exposure to water related pathogens, chemical hazards and cyanotoxins. The final aim is provide knowledge-based elements for more focused adaptation measures.