Global climate change significantly alters environmental and health dynamics, posing a major 21st-century public health threat. Diseases commonly transmitted through water and/or food (diarrhea, cholera, dysentery) are particularly sensitive to these changes. While numerous studies have investigated the climate impacts on waterborne diseases, a critical assessment of the applied methodologies and the consistencies of their outcomes is lacking. This systematic review synthesizes the impact of climate change on waterborne diseases, focusing on analytical methods and predictive models used to explain disease presence or abundance. We further evaluate the strengths and limitations of each approach, identifying key gaps for future research. We analyzed 78 indexed research articles published between 1996 and 2023. Our findings demonstrate that diverse climate-related extreme events, including precipitation, flooding, and drought, substantially impact waterborne disease incidence. Additionally, temperature, salinity, humidity, sunshine duration, wind patterns, and specific water quality parameters play significant roles, with regional variations observed. Sensitivity analysis methods and mathematical models are employed to assess sensitivities, quantify correlations, examine impacts, and predict risks. Based on these findings, we urge future research to prioritize elucidating mechanisms and developing models that leverage climate data to predict disease presence or abundance accurately and quantitatively.