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Different methods for estimating the total phosphorus (TP) reference conditions of lakes have rarely been compared. This work tests the uncertainty and accuracy of the most frequently used approaches (Morpho-edaphic index -MEI-, export coefficient, diatoms and pigment-inferred TP models) for 35 subalpine lakes. Furthermore, we propose a new process-based watershed approach that was tested on a subalpine environment and consists of combining a space for time substitution with a space for space substitution. The possible presence of uncontaminated or less contaminated environments inside or next to the watershed can be exploited by training a hydrological transport watershed model according to the uncontaminated conditions and then applying the calibration to the entire watershed, which reconstructs a natural or semi-natural TP load scenario. We found that the root mean square error (RMSE) for the …