Groundwater is the main source of water for more than 2 billion people worldwide. In southern Brazil, the Crystalline Basement Aquifer System is composed of strategic groundwater reservoirs. Groundwater is mostly taken from shallow wells, and it is often used without any treatment, which poses a risk to public health. The present study aims to evaluate shallow groundwater quality and the geochemistry of shallow and deep groundwater located in the municipality of Canguçu, southern Brazil. The physicochemical and microbiological parameters of groundwater samples collected from shallow wells were monitored and analyzed using ANOVA variance analysis and water quality index (CCME WQI) approaches. Also, the results were compared with secondary data from deep wells. The monitored shallow wells had thermotolerant coliforms, Escherichia coli, pH, potassium, manganese, iron, and nitrate in disagreement with the guidelines of the World Health Organization. Moreover, variance analysis showed that the parameters temperature, dissolved oxygen, pH, chloride, and magnesium were the most influenced by seasonal variations. According to the CCME WQI, most samples had good quality (60%), 28% had fair quality, and 12% had poor quality. In addition, the field campaigns with higher precipitation rates also presented fair quality. Therefore, most of the shallow groundwater quality is affected by surface pollutants from the urban area, aggravated in rainy periods. Whereas deep groundwater is influenced by geochemistry mechanisms. The results revealed the risk of water consumption for public health and the urgent need for better maintenance of these wells and water treatment implementation.