Climatic changes have altered the water cycle, leading to more frequent occurrences of natural disasters, such as floods. In such events, quality of life is compromised due to environmental changes and widespread of pathogens. Unfortunately, scientific knowledge on bacteria behavior during different hydrological events is still scarce, and such knowledge is essential for the decision-making process regarding flood prevention and mitigation measures. Therefore, the present study aimed to investigate the changes in the enterobacteriaceae community and toxicity from river water samples collected during hydrological cycles over the rainy and dry seasons and on flood events. Additionally, a principal component analysis was performed to verify the relation between microbial and chemical profiles and the hydrological events. Results showed the presence of 153 enterobacteriaceae from 32 different species and of toxic substances on water samples collected during all hydrological events. During the rainy period, the Escherichia coli concentration increased along the river, and during flood events, the diversity of bacteria increased. However, bacterial diversity was not statistically associated with a specific hydrological event. These events can happen all around the world, and due to climatic changes associated with overpopulated unplanned areas, new flood-prone areas can appear rapidly, favoring the occurrence of waterborne outbreaks.