The implementation of the European Union Water Framework Directive (WFD) presents an important methodological challenge for countries whose established environmental monitoring systems are not yet fully harmonised with WFD compatible surface water body delineation and assessment structures. This situation is particularly relevant for EU candidate countries, where existing station-based monitoring programmes must increasingly support integrated river basin assessment and alignment with the environmental acquis. This study addresses this challenge by developing a robust composite Surface Water Quality Index (SWQI) capable of integrating existing monitoring observations into a consistent quantitative river basin assessment while accommodating incomplete spatial harmonisation of water body delineation. The proposed framework integrates six physicochemical parameters—dissolved oxygen (DO), biochemical oxygen demand (BOD₅), ammonium (NH₄), nitrite (NO₂), nitrate (NO₃) and total phosphorus (P-total)—through normalization, weighting and aggregation into a common 0–100 scale. A bounded continuous normalization approach was developed for observations exceeding Class V boundaries, preserving information on the severity of extreme observations while constraining scores within the defined scale. The framework was applied to 33 monitoring stations with complete six parameter datasets across five Albanian river basin reporting units. Mat recorded the highest basin level SWQI (98.79), followed by Drin-Bunë (97.40), Shkumbin (94.29) and Seman (93.33), whereas Ishëm-Erzen recorded the lowest value (68.54). Robustness testing demonstrated that the basin ranking remained unchanged across alternative parameter weighting schemes, aggregation methods and normalization treatments, indicating that the principal spatial pattern was not dependent on a single methodological assumption. Comparison with the national environmental assessment further demonstrated that the SWQI provides complementary information rather than reproducing or replacing regulatory ecological status classification. The study demonstrates that station-based monitoring observations can be transformed into a transparent and reproducible basin level assessment even where WFD oriented spatial harmonisation is still progressing. Beyond Albania, the framework has potential as a transferable methodological approach for EU candidate countries undergoing alignment with the WFD acquis, particularly where established monitoring systems need to be progressively integrated with WFD compatible water body delineation and assessment structures.