<p>Standardizing water quality assessment is a global challenge, particularly in semi-arid regions, where climatic variability and anthropogenic pressures intersect. This study introduces WQI-TR v1, a novel multi-parameter water quality index designed to align specifically with the European Union’s Water Framework Directive (WFD). To demonstrate its utility, the index was applied to the Konya Closed Basin (Türkiye), a semi-arid region characterized by high levels of endemism and extreme hydrological stress. Surface water samples (n = 45) were collected during the wet and dry seasons of 2024 across three sub-basins in the Konya Closed Basin, Türkiye. Hydrochemical facies were identified using Piper and Gibbs diagrams. The WQI-TR was constructed using four sub-indices: organic pollution (35%), nutrient pollution (30%), secondary stressors (23%), and toxic contaminants (12%). Validation was performed via multiple linear regression (R²_adj = 0.97) and Principal Component Analysis. Hydrochemical characterization revealed a distinct three-stage facies evolution across the basin, transitioning from a lithologically controlled calcium-bicarbonate (Ca-HCO₃) signature in the recharge zones to an alkali-sulfate character in the terminal sink, driven by progressive evaporative concentration and calcite precipitation. WQI-TR scores classified most sites as "Good" or "Moderate," although localized "Poor" conditions were identified. Statistical analysis confirmed that secondary stressors (salinity) and toxic contaminants were driven by spatial/basin factors, whereas organic pollution was significantly influenced by seasonal low-flow conditions (p &lt; 0.001). Nutrient pollution remained a chronic, stationary pressure across all sites. The integration of this index into a web-based application provides stakeholders with a reproducible and standardized tool to monitor and manage water quality in water-scarce ecosystems.</p>