Climate change is a significant and growing determinant of global public health, with profound implications for waterborne diseases. This review examines the specific pathways through which climate variability and change exacerbate the burden of microbial waterborne diseases in Nigerian communities. Evidence indicates that increased temperatures enhance the survival and replication rates of enteric pathogens like Vibrio cholerae in aquatic environments. Furthermore, extreme hydrological events—including intensified seasonal flooding and more frequent droughts—directly compromise water quality and accessibility. Flooding leads to the widespread contamination of drinking water sources with fecal matter, triggering outbreaks of cholera and other diarrheal diseases, particularly in vulnerable regions such as the Niger Delta and northeastern Nigeria. Conversely, droughts concentrate pathogens in limited water supplies and force reliance on unsafe alternatives. These climate-driven risks are amplified by Nigeria’s pre-existing challenges, including fragile water and sanitation infrastructure, rapid urbanization, and high poverty levels. The synthesis concludes that climate change acts as a threat multiplier, systematically undermining water security and elevating community exposure to waterborne pathogens. To mitigate this escalating health threat, there is an urgent need for integrated adaptation strategies that combine climate-resilient water, sanitation, and hygiene (WASH) interventions, strengthened disease surveillance systems, and community-based public health education.