The North region is the second region in Brazil with the highest incidence rate of diarrheal diseases in children under 5 years old. The aim of this study was to investigate the relationship between rainfall and water level during the rainy season principally with the incidence rate of this disease in a southwestern Amazon basin. Rainfall estimates and the water level were correlated and both of them were correlated with the diarrheal incidence rate. For the Alto Acre region, 2 to 3 days' time-lag is the best interval to observe the impact of the rainfall in the water level (R = 0.35). In the Lower Acre region this time-lag increased (4 days) with a reduction in the correlation value was found. The correlation between rainfall and diarrheal disease was better in the Lower Acre region (Acrelândia, R = 0.7) and rainfall upstream of the city. Between water level and diarrheal disease, the best results were found for the Brasiléia gauging station (Brasiléia, R = 0.3; Epitaciolândia, R = 0.5). This study's results may support planning and financial resources allocation to prioritize actions for local Civil Defense and health care services before, during and after the rainy season.