Satellite images are essential tools for monitoring aquatic ecosystems and assessing water quality, as they enable the measurement of parameters such as chlorophyll-a (Chl-a) concentration, phycocyanin (PC), and cyanobacteria density. These indicators aid in evaluating eutrophication processes and detecting cyanobacteria in aquatic ecosystems. This study utilized field data and images captured by the Sentinel-2 sensor from 2015 to 2022 to investigate the Jaguari-Jacareí reservoirs (JAG-JAC). Two atmospheric corrections from the Case 2 Regional Coast Color (C2RCC) processor, namely C2X and C2XC, were applied, and algorithms were developed to estimate the parameters using both in situ data measurements and reflectance data extracted from the images. For Chl-a concentration, the dataset was divided into two blocks: one for model calibration (70% of the data) and the other for validation (30% of the data). As for PC, the entire dataset was utilized to calibrate the model, and validation was conducted through cross-validation using the Automated Radiative Transfer Model Operator (ARTMO) software. Cyanobacteria density was indirectly estimated from the Chl-a concentrations determined in the field samples, as these variables exhibited a strong correlation, also validating the model previously proposed for the Cantareira system for estimating cyanobacteria density from Chl-a data. Additionally, the automatic chlorophyll-a products (con_chla) derived from the C2X and C2XC processors were validated. The findings revealed that the C2X processor exhibited the greatest potential for estimating water quality parameters. It was observed that the most effective algorithms were derived using the R705/R665 band ratio for Chl-a and the R705/R490 ratio for PC. For cyanobacteria density, the optimal algorithm was established based on the relationship between cyanobacteria density and Chl-a using the data obtained in this study.