Water is scarce in semi-arid regions due to environmental limitations; this situation is aggravated by changes in land use and land cover (LULC). In this respect, the basic ecological functions of Permanent Preservation Areas (PPAs) help to maintain water resources. The aim of this study was to evaluate the relationship between the LULC and water quality in PPAs in a semi-arid watershed, from 2009 to 2016. The following limnological data were analyzed: chlorophyll-a, transparency, total nitrogen and total phosphorus. The changes in LULC were obtained by classifying images from Landsat 5, 7 and 8 into three types: Open Dry Tropical Forest (ODTF), Dense Dry Tropical Forest (DDTF) and Exposed Soil (ES). Spearman correlation and principal component analysis were applied to evaluate the relationships between the parameters. There was a significant positive correlation between DDTF and the best limnological conditions. However, ES showed a significant negative relationship with transparency and a positive relationship with chlorophyll-a, indicating a greater input of sediments and nutrients into the water. The PCA corroborated the results of the correlation. It is therefore essential to prioritize the preservation and restoration of the vegetation in these sensitive areas to ensure the sustainability of water resources. Future studies should assess the impact of specific human activities, such as agriculture, deforestation and livestock farming, on water quality in the PPAs.