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Morbimortality due to infectious diarrheal diseases still is a serious health issue in Brazil and is highly related to factors such as weather, environment, and people's life conditions. This study aimed to analyze the relationship between hospitalization rates due to infectious diarrheal diseases among the population of the municipality of Rio Branco (AC), Brazil and precipitation, river level, humidity and temperature between 2000 and 2013. Data were retrieved from the Hospital Information System of the SUS (Unified Health System), the National Institute of Meteorology and the National Water Agency. Multiple Poisson and negative binomial regression models were adjusted. Results showed that there is a positive association between hospitalization due to infectious diarrheal diseases and the level of the Acre river (RR: 1.07; CI 95%: 1.04 to 1.1); these hospitalization rates fell 14% between 2000 and 2013 (RR: 0.86; CI 95%: 0.85 to 0.87). The most vulnerable group was the age group of less than 1 year of age. This study showed the vulnerability of an Amazonian city to climate variability and its respective epidemiological influence on the incidence of hospitalizations due to infectious diarrheal diseases.