In dry areas, the need for irrigation to ensure agricultural production determines the use of all available water sources. However, the water sources used for irrigation are often contaminated by untreated or minimally treated wastewater. Microbial risks from reusing wastewater for vegetable irrigation can be addressed by installing environmental barriers that pathogens must cross to reach humans in the reuse system. Knowledge of pathogen flows inside the system and pathogen removal potential is the first step towards devising a risk management strategy. This study assessed microbe prevalence in farming systems in the Bolivian highlands that use wastewater-polluted sources for irrigation of lettuce. Samples of soil, lettuce and different water sources used in the farming systems were taken during one crop season and concentrations of coliphages, Escherichia coli and helminth eggs were measured. The results showed high spread of these microorganisms throughout the whole system. There was a significant correlation between microbial quality of water and of the harvested produce for several microorganisms. The microbial prevalence in protected shallow wells was found to be significantly lower than in other water sources. These findings can help formulate feasible risk management strategies in contexts where conventional technologies for microbial removal are not possible.