Surface water quality has increasing importance worldwide and is particularly relevant in the semiarid North-Central Chile, where agriculture and mining activities are imposing heavy pressure on limited water resources. The current study presents the application of a water quality index in four watersheds of the 29°-33°S realm for the period 1999-2008, based on the Canadian Council of Ministers for the Environment approach and the Chilean regulation for irrigation water quality. In addition, two modifications to the index are tested and a comprehensive characterization of the existing monitoring network is performed through cluster analysis. The basins studied show fairly good water quality in the overall, specially the Limarí basin. On the other hand, the lower index values were obtained for the headwaters of Elqui, associated with the El Indio mining district. The first modification of the indicator (i.e., to consider parameters differentially according to their effect on human health or the environment) did not produce major differences with respect to the original index, given the generally good water quality. The second modification (i.e., to consider as threshold values the more restrictive figures derived from a set of regulations) yielded important differences in the indicator values. Finally, an adequate characterization of the monitoring network was obtained. The results presented spatial coherence and the information can be used as a basis for the optimization of the monitoring network if required.