In a rural watershed in Chile, the scarce groundwater available represents almost the only water source both for agriculture and domestic use. This water has microbiological quality problems, which result in an agricultural and local economic development constraint. Contamination can come from punctual or diffuse sources. Characterizing the microbiological quality of groundwater allows both to identify sources from the point of view of whether they are point or non point -thus facilitating their reduction or elimination- and to determine health hazards likely to affect the population in the area under study. This study aimed to improve the state of knowledge on the microbiological quality of groundwater at a rural watershed. Forty two wells were seasonally analyzed over a one-year period. The indicators microorganisms -total coliforms, fecal coliforms and fecal streptococci- were quantified. The study of the probable origin of the indicators was undertaken using the fecal coliform to fecal streptococci ratio, biochemical identification of enteric bacteria, and somatic coliphages detection as presence of human enteric virus indicator. Temporal contamination dynamics was determined with statistical analysis of indicator organism concentration. Results suggest that the main source of fecal contamination is of animal origin, a diffuse one. Concentrations of bacterial indicators have a temporal basis showing variable levels among seasons, with a higher concentration in the rainy one. All analyzed wells contain opportunistic pathogens.