In regions under development and facing recurrent droughts, increasing the area of irrigated agriculture may create additional disruption in water resources management. The present study was focused on three river sub-basins with the highest agricultural intensity (S. Miguel, Ribeira Seca and S. Domingos) in Santiago Island (Cape Verde). Sets of wells were selected to evaluate the influence of salinization and agriculture practices on the hydrochemistry. This assessment was performed by using data from the bibliography (2003) and a recent campaign (2016). The water chemistry indicates lower mineralization in the S. Miguel sub-basin. Nitrates and nitrites, typically associated with diffuse pollution, are present in all sub-basins, but with varying patterns. Additionally, sodium chloride waters occur in all the three sub-basins, especially those closest to the coastline. In turn, a bicarbonate-magnesium facies was identified in S. Domingos, at the furthest point from the coast, indicating a geological control. The comparison between the two periods suggests a decrease in water quality. The rising extension of the irrigation area associated with aridity should intensify the already observed soil salinization. Thus, the present review highlights the strategic importance of water monitoring at the basin level as a management tool for resources preservation in insular arid and developing regions.