Although the average municipal water coverage in Taiwan is quite high, at 93.91%, only around half of the residents in the Pingtung Plain use tap water originating from the Taiwan Water Corporation to meet their needs. This means the exploitation of a substantial amount of groundwater as a source of water to meet drinking, agriculture, aquaculture, and industry requirements. Long-term groundwater quality surveys in Taiwan have revealed obvious contamination of the groundwater in several locations in the Pingtung Plain, with measured concentration levels of some groundwater quality parameters in excess of the permissible levels specified by the Taiwan Environmental Protection Administration. Clearly, establishing a sound plan for groundwater quality protection in this area is imperative for maximizing the protection of human health. The inappropriate use of hazardous chemicals and poor management of land use have allowed pollutants to permeate through unsaturated soil and ultimately reach the underlying shallow unconfined groundwater system. Thus, the quality of the water stored in shallow aquifers has been significantly affected by land use. This study is designed to characterize the relationship between groundwater quality and land use in the Pingtung Plain. This goal is achieved by the application of factor analysis to characterize the measured concentrations of 14 groundwater quality parameters sampled from 46 observation wells, the area percentages for nine land use categories in the neighborhood of these 46 observation wells, and the thicknesses of four unsaturated types of soil based on core samples obtained during the establishment of 46 observation wells. The results show that a four-factor model can explain 56% of the total variance. Factor 1 (seawater salinization), which includes the groundwater quality parameters of EC, SO42−, Cl−, Ca2+, Mg2+, Na+, and K+, shows a moderate correlation to land used for water conservation. Factor 2 (nitrate pollution), which includes the groundwater quality parameters of NO3−-N and HCO3−, shows a strong correlation to land used for fruit farming and a moderate correlation to the thickness of the gravel comprising unsaturated soil. Factor 3 (arsenic pollution), which is composed of groundwater quality parameters of total organic carbon (TOC) and As, is very weakly affected by land use. Factor 4 (reductive dissolution of Fe3+ and Mn2+), which involves Mn2+ and Fe3+, is weakly impacted by land use. Based on a geographic visualization of the scores for the four different factors and the patterns for land use, we can demarcate the areas where the groundwater in shallow unconfined aquifers is more vulnerable to being polluted by specific contaminants. We can then prioritize the areas where more intensive monitoring might be required, evaluate current land use practices, and adopt new measures to better prevent or control groundwater pollution.