Integrated analyses of the qualitative and quantitative aspects of aquatic ecosystems play an important role in decision making, which is linked to water resources management and promotion of ecosystem services. However, the possible advantages of such integration are still hampered by basic aspects, such as high uncertainties due to the partial and non-synchronized monitoring of discharges and observed concentrations of water quality variables. The lack of data has been limiting the adequate representation of a more accurate hydrological regime, which is in turn possibly affected by the potential effects of land use and size of drainage areas. The aim of this research was to discuss the advantages of the integrated analysis of qualitative and quantitative data from water bodies. Under different specific discharge regimes (L.s -1.km-2), we assessed the total phosphorus (TP, t.day-1 .km-2) and thermotolerant coliforms’ (TC, CFU.day-1.km -2) specific loads in rivers with different drainage areas (27-26,500 km 2) and land uses. We compared such loads with the admissible specific loads for these variables, which were estimated based on long-term average discharges and water quality guidelines (i.e., Brazilian environmental standards). Based on data from 2001-2013, we sought to contribute to the qualitative and quantitative analysis of surface waters, focusing on the discussion of the results on critical thresholds of duration and critical loads and discharges. The results showed the existence of significant time intervals with conflicts between the specific admissible and observed loads. This non-compliance varied between 10 and 100% of the duration of the regime for TP, and between 25 and 100% for TC, with a more critical situation observed in rivers with smaller drainage areas. The critical loads ranged from 1 10-4 to 8 10-3 t.day-1.km-2 (TP) and 1 10-2 to 1 10-1 CFU.day-1.km-2 (TC). Although a relatively limited dataset was considered (total N=1,402), the significant variations in discharges and critical loads highlighted the need for considering how these dynamics would affect the traditional methodology for estimating ecological flows, whose current approach is almost exclusively quantitative.