Groundwater contaminants are recognized as a primary threat to the persistence of subterranean organisms that inhabit karst systems. However, contaminants’ impacts are poorly understood due to the absence of knowledge regarding their dispersion through these environments and an incomplete understanding of taxa ecologies and their toxicity thresholds. The Alabama Cave Shrimp, Palaemonias alabamae, is an endemic stygobiont restricted to five cave systems in Northern Alabama, including Bobcat Cave. To facilitate the characterization of threats to this species, the Geological Survey of Alabama has collected biological and hydrogeological data from Bobcat Cave for over three decades. Using this comprehensive dataset, the objectives of this study were to (1) evaluate and characterize ecohydrogeological relationships for the population of P. alabamae in Bobcat Cave and (2) evaluate contaminant concentration-cave water elevation relationships to describe the extents to which seasonal runoff and deep groundwater contamination impact water quality in Bobcat Cave. Relationships between Alabama Cave Shrimp abundance and hydrogeological characteristics and relationships between water quality and cave water elevation were evaluated by building general additive models. Shrimp abundance was best described as an outcome of a chloride-cave water elevation interaction. Seasonal, cave water elevation-concentration relationships were detected for nitrate, lead, cadmium, and fluoride while nonseasonal relationships were detected for chloride, phosphorus, nitrate, and fluoride. Major findings indicate (1) that chloride may act as a subsidy or stressor on this species and (2) there was no evidence that chloride concentrations in Bobcat Cave varied by season; instead, this solute is becoming more diluted over time suggesting the contaminant’s origin may be a deep groundwater source. Additional sampling is needed to validate these findings and to identify stressors and their toxicity levels in the other cave systems. The work performed in this study addresses critical knowledge gaps that must be overcome to ensure future conservation efforts targeting this imperiled species are successful.