The Titicaca Lake is the most important water resource over the Andean plateau and the ecological equilibrium of this region is nowadays perturbed by recent changes in land use and management practices. The Katari watershed encompasses mining area, cities representing over 1.2 million habitants, and agricultural zones before ending in Cohana bay in the Titicaca Lake. Cohana Bay is known to be one of the most eutrophic bay of the Titicaca Lake. The objective of the study was to evaluate the impact of anthropic activities along the watershed on the river quality and on the bacterial diversity. Both mining activities and release of wastewater in river systems impacts greatly the surface water quality, with level of As exceeding limits for drinking water, and phosphate over the European guidelines for bad quality rivers. Antibiotic from the sulfonamide family was detected in the watershed in high concentrations downstream of the two main cities and bacterial resistance occurred in nearly all the sampled water points.