The potability of water, including underground sources, is constantly affected by human activities. To assess water quality and water security in rural and urban areas of southern Brazil, a quantitative, retrospective analysis of water samples collected monthly by the Brazilian health authorities (19,687 samples from 2013 to 2021) was performed. In rural areas, 5,979 water samples (77.54%) were found to be contaminated by coliform bacteria and 3,431 (44.50%) by Escherichia coli. In addition, 1,616 (20.95%) of the contaminated samples were significantly correlated with rainfall amount. In urban areas, 1,268 (10.95%) of the samples contained coliform bacteria and 293 (2.53%) of these samples contained E. coli, with the factor of rainfall associated with 1,081 samples (9.33%) with bacterial contamination. In terms of physicochemical parameters, turbidity exceeded the national standard (5 uT) in 448 (2.32%) samples and fluoride fell below the required level (0.8 mg/L) in 106 samples (0.54%). The presence of free residual chlorine (0.2-2.0 mg/L) was verified in 846 samples (14.38%) in rural areas and in 10,825 samples (56.13%) in urban areas. These results suggest a strong association between rainfall factors and physicochemical alterations, as well as the risk of greater microbial contamination of water for human consumption.