Rotavirus (RV) it’s the agent of one of the main causes of severe viral gastroenteritis in the pediatric population, being responsible for a significant portion of deaths related to diarrhea among children under five years. RV are identified as a potential reference pathogen and it is known that the persistence and infectivity of the viral particles can be related to environmental factors. The aim of the study was to identify and correlate the presence of Rotavirus in collective and individual water sources (deep tubular wells, shallow tubular wells, shallow dug wells, springs, surface water, rainwater stored in cisterns and water trucks that were collected from surface water) of rural communities in the state of Goiás, with the seasons in which the collections were made (rainy and dry season). For this, 86 water samples in the dry period and 160 samples in the rainy period were collected. Concentration of water samples, extraction of viral genetic material, cDNA synthesis and molecular tests (qPCR) were performed. When analyzing the presence of RV in the samples in relation to the period studied, RV was found to be more prevalent in the dry season (54.7%) than in the rainy season (20%), showing a strong statistical association with the dry season (p-value < 0.001). The proportion of positive samples in the dry period, considering the type of source, resulted in higher in Shallow dug wells (p-value <0.001), higher in surface waters (p = 0.001) and higher in spring water (p-value = 0.02). The presence of pathogenic microorganisms in water is a public risk problem, enabling the emergence of outbreaks, endemics and epidemics. In the present research, there was an association among the presence of Rotavirus and the dry period of the year, when compared to the rainy period. Describing or identifying the seasonal behavior of pathogens is important for prevention and attention to water treatment and help in the monitoring of the virus in the water sources.