The Water Quality Index (WQI) is widely applied for long-term monitoring and inter-basin comparison of surface water quality; however, its interpretation may vary depending on basin characteristics and hydrological organization. This study evaluates WQI behaviour in three Lithuanian river basins (Nemunas, Mūša, and Venta) representing contrasting spatial scales and hydrological integration during 2001-2024.
Annual monitoring data of key physicochemical parameters were analysed using variability metrics and principal component analysis (PCA) to assess the relationship between WQI and dominant hydrochemical gradients. Although mean WQI levels were similar among basins, marked differences in structural variability were observed. In the large, hydrologically integrated Nemunas basin, the first principal component explained 44.8% of total variance, indicating stronger dimensional consolidation. Smaller basins exhibited more fragmented multidimensional organization. The correlation between WQI and the dominant gradient ranged from strong (|r| = 0.82-0.86) in the Nemunas and Mūša basins to moderate (|r| = 0.40) in the Venta basin. Significant hydrological control of the primary gradient was detected only in the largest basin (ρ = –0.48, p = 0.001).
These findings demonstrate that WQI performance is conditioned by basin-scale structural organization. Integrating composite indices with multivariate analysis enhances the interpretation of long-term monitoring data and supports more reliable inter-basin comparisons.