This study introduces a novel Groundwater Pollution Index (GPI) formulated through compositional data analysis (CoDa) and robust principal component analysis (RPCA) to enhance groundwater quality assessment. Using groundwater quality monitoring data from sites impacted by the 2010–2011 foot-and-mouth disease outbreak in South Korea, CoDa uncovers critical hydrochemical differences between leachate-influenced and background groundwater. The GPI was developed by selecting key subcompositional parts (NH4+-N, Cl−, and NO3-−N) using RPCA, performing ilr transformation, and normalizing the results to environmental standards, thereby offering a more precise and reliable pollution assessment. Validated against government criteria, the GPI demonstrated its potential as an alternative assessment tool, confirmed by receiver operating characteristic (ROC) curve analysis. The study underscores the importance of CoDa, especially the isometric log-ratio (ilr) transformation, in overcoming the limitations of traditional statistical methods by focusing on the relative nature of hydrochemical data. By bridging a methodological gap in groundwater assessment, the GPI represents a significant advancement in groundwater quality monitoring and management. Our results emphasize the importance of considering the compositional nature of environmental data and show the utility of multivariate statistical methods in enhancing the precision and reliability of pollution assessments.