Quantification of water quality (WQ) is an integral part of scientifically based water resources management. The main objective of this study was comparative analysis of two approaches applied for quantitative assessment of WQ: the trophic level index (TLI) and the Delphi method (DM). We analyzed the following features of these conceptually different approaches: A. similarity of estimates of lake WQ; B. sensitivity to indicating disturbances in the aquatic ecosystem structure and functioning; C. capacity to reflect the impact of major management measures on the quality of water resources. We compared the DM and TLI based on results from a series of lakes covering varying productivity levels, mixing regimes and climatic zones. We assumed that the conservation of aquatic ecosystem in some predefined, “reference”, state is a major objective of sustainable water resources management in the study lakes. The comparison between the two approaches was quantified as a relationship between the DM ranks and respective TLI values. We show that being a classification system, the TLI does not account for specific characteristics of aquatic ecosystems and the array of different potential uses of the water resource. It indirectly assumes that oligotrophication is identical to WQ improvement, and reduction of economic activity within the lake catchment area is the most effective way to improve WQ. WQ assessed with the TLI is more suitable for needs of natural water resources management if eutrophication is a major threat. The DM allows accounting for several water resource uses and therefore it may serve as a more robust and comprehensive tool for WQ quantification and thus for sustainable water resources management.