Continuous series of nutrient loads released into a water body are essential for nutrient budgeting, water quality modelling and watershed management activities. A quintessential example of pursued data are the series of total nutrient loads flowing from multiple tributaries into a lake. However, except for extraordinary cases in which high-frequency monitoring (HFM) stations are installed for both discharge and concentrations, measured nutrient loads are available on a discrete basis. Such observations are typically obtained by governmental agencies for environmental monitoring purposes, with an at best monthly resolution, yet commonly with gaps spanning years. Usually, monitoring activities are limited to major inflows, neglecting minor ones. However, the latters can play a more relevant role in nutrient load budgets than in hydrological ones, in response to different natural features and pollution among tributary watersheds. In this work, we present a methodology we developed to estimate long-term series of total nutrient loads flowing into a water body, employing as case study Lake Como, a large deep lake in the Italian Alps with manifold monitored and unmonitored tributary watersheds. The method uses observed long-term relationships between discharges and concentrations (Q – C) and available discharge measurements and hydrological estimations to estimate continuous load series for the monitored basins. For the unmonitored watersheds, Q – C relationships are estimated from those of the monitored basins, given the observed dependence of the power-law coefficients on basin hydromorphological parameters. This equals to extending the regionalisation approach applied in hydrology for rainfall and discharges to the ecohydrological field for nutrient load estimation. The application of the method to the case study led to overall annual load estimations congruent to traditional techniques and revealed interesting Q – C watershed dynamics at interannual time scales which could not be disclosed through previous approaches. This work represents an exploratory development and application of ecohydrological regionalisation techniques, whose future development is fostered.