<![CDATA[Lake Sentani is the largest lake in Papua and an important raw water source facing pressure from residential expansion, agricultural runoff, domestic wastewater, and small-scale mining. This study developed and internally evaluated the Rational Water Quality Index (RWQI), integrating the Regulatory Violation Index (RVI), Toxicological Severity Score (TSS), and Limnochemical Similarity Coefficient (LSC). Data were collected from 45 sampling points across four limnological zones over three seasonal periods. The first-season dataset (n = 45) was used to develop the PCA-based LSC structure, while the subsequent two seasons (n = 90) assessed its temporal stability without recalibration. Overall performance was evaluated using classification accuracy, ROC/AUC, structural coherence, and consistency with trophic conditions. RWQI achieved 91.56% classification accuracy, AUC = 0.980, and R² = 0.989, outperforming SWQI, OWQI, and the Pollution Index. Spatial analysis identified the Harapan and Flafow River littoral zones as priority areas (RWQI 38.2–43.7, Poor), while the pelagic center maintained Good quality (RWQI 84.2). RWQI shows potential as an adaptive framework for tropical lake assessment, but independent external validation remains necessary before broader standardization.]]>
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