Although water availability depends both on qualitative and quantitative aspects, most studies focus only on one of these. Therefore, the goal here is to relate water quality and quantity with the construction of Load Duration Curves (LDC) and to estimate E. coli load patterns in different flow conditions, seasons, and positions of two sub-basins of the Doce watershed (Brazil): Piracicaba and Piranga. A novel methodology is proposed in which the Burr XII distribution is adjusted to the LDC to compare all observed loads to their respective Total Maximum Daily Load (TMDL), allowing the estimation of the relative difference (RD) between these. Higher values of RD were observed for low flows for the Piracicaba basin, more urbanized, where point sources of pollution are the primary concern, reaching up to 99% of needed load reduction. In the Piranga basin, more agricultural, there was a broader RD variation, from 9% to 97% load reduction needed, which is an evidence of point sources of pollution combined with non-point sources. The new methodology can be used to estimate the load reduction of any pollutant and can be used by environmental agencies to identify effective practices to minimize and control pollution in different locations of the basins.