A major objective for domestic wastewater treatment using waste stabilization pond systems is the removal of pathogenic microorganisms. Traditional evaluation parameters for faecal contamination are the total and faecal coliforms. However, epidemiological studies, environmental resistance and the behaviour in the treatment systems, show that viruses are an important disease agent and even more resistant to disinfection than bacteria. Therefore, it is important to introduce viruses as a faecal indicator and to compare them with the traditional bacterial indicators. A waste stabilization pond system was evaluated in the municipality of Chocontá, Cundinamarca (Colombia), for the removal of faecal indicators (such as Escherichia coli, Streptococcus faecalis, Clostridium perfringens) and viruses like F+, somatic and Bacteroides fragilis phages. The system includes two facultative ponds in series with a flow of 1555 m3/day. Samples were collected at the entrance of the system, in the two ponds and from the final effluent. Results show a decrease between 0.3 and 4.7 logarithmic units in the bacterial indicators and between 1 and 4.6 logarithmic units with viral indicators.