Reservoirs have been subject to anthropogenic stressors, becoming increasingly degraded. The evaluation of ecological potential in reservoirs is remarkably challenging, and consistent and regular monitoring using the traditional in situ methods defined in the WFD is often time- and money-consuming. Alternatively, remote sensing offers a low-cost, high frequency, and practical complement to these methods. This paper proposes a novel approach, using a C2RCC processor to analyze Sentinel-2 imagery data to retrieve information on water quality in two reservoirs of Portugal, Aguieira and Alqueva. We evaluate the temporal and spatial evolution of Chl a and total suspended solids (TSS), between 2018 and 2020, comparing in situ and satellite data. Generally, Alqueva reservoir allowed lower relative (NRMSE = 8.9% for Chl a and NRMSE = 21.9% for TSS) and systematic (NMBE = 1.7% for Chl a and NMBE = 2.0% for TSS) errors than Aguieira, where some fine-tuning would be required. Our paper shows how satellite data can be fundamental for water-quality assessment to support the effective and sustainable management of inland waters. In addition, it proposes solutions for future research in order to improve upon the methods used and solve the challenges faced in this study.