An improved methodology first proposed by Yannopoulos (2009) for the determination of river discharges is presented. It aims to reduce time, personnel and cost of campaigns required in the application of water quality monitoring programs and the programs of measures, as well as of management plans, imposed by the water management legislation valid for the river watersheds. At river cross-sections without permanent equipment, it is common to employ quick methods of low reliability to measure the river discharge. Then, a suitable correction may be followed in order to obtain more reliable values compared to initial discharge estimates used to calculate the desired pollution loads. The proposed methodology is still improved through the consideration of a possible latent discharge and applied to Alfeios River, where simultaneous measurements of the river discharge and quality characteristics were available.