The use of swine effluents as a biofertilizer is an alternative to chemical fertilizers and to water demand in dry season. Nevertheless, fertigation studies usually focus on the plant demand and the soil nutrition parameters, mainly physic-chemical ones. This work aimed to evaluate the impacts of fertigation with swine effluents treated in the microbial quality of groundwater from the phreatic aquifer in two lots on Campanário settlement, on the city of São Gabriel do Oeste, MS, Brazil. Microbial analyses were carried out on groundwater samples from four piezometer and two supply wells using the Colilert system to quantify total coliform and Escherichia coli. Samples were collected during twelve months. The results indicate groundwater contamination by bacteria of the coliform group, according to the drinking water Brazilian standards and its spatial distribution from the point sources to a spreading area in accordance with groundwater flow. Therefore, water disinfection is strongly recommended for drinking purposes. Despite having a strong correlation with groundwater microbial contamination, especially in rainy season, fertigation with swine effluents seem not to be the only source of pathogens in the phreatic aquifer. However, high total coliform values in dry season samples could be assigned to the fertigation.