Eutrophication, a global concern, impacts water quality, ecosystems, and human health. It’s crucial to monitor algal blooms in freshwater reservoirs, as they indicate the trophic condition of a waterbody through Chlorophyll-a (Chla) concentration. Traditional monitoring methods, however, are expensive and time-consuming. Addressing this hindrance, we developed models using remotely sensed data from the Sentinel-2 satellite for large-scale coverage, including its bands and spectral indexes, to estimate the Chla concentration on 149 freshwater reservoirs in the state of Ceará, Brazil. Several machine learning models, including k-nearest neighbours, random forests, extreme gradient boosting, the least absolute shrinkage, group method of data handling (GMDH), and support vector machine models were trained and tested. A stepwise approach determined the best subset of input parameters. The best-performing model was the GMDH, achieving an R2 of 0.91 and RMSE of 20.38 mg/L, which is a value consistent with the ones found in the literature. Nevertheless, the predicted Chla concentration values were most sensitive to the red, green, and near infra-red bands.