Water clarity, measured by its transparency and turbidity, is a crucial characteristic for evaluating water quality. Water transparency could be defined as the extinction of light along the water column, conventionally estimated by Secchi disk depth. Remote sensing, particularly using Sentinel-2 imagery, has proven to be a valuable tool for monitoring water transparency in different bodies of water. In this study, a new algorithm was developed to estimate the Secchi disk depth in the Albufera de Valencia, a highly eutrophic coastal lagoon in Spain, using Sentinel-2 mission data. Three optical models (R490/R560, R490/R705, and R560/R705) were assessed for Secchi disk depth estimation. The R560/R705 model exhibited the best results and was selected for algorithm development and validation. The R560/R705 model achieved R² values of 0.6149 and 0.916 during calibration and validation, respectively, while the other models achieved an R² of 0.2805 (R490/R705) and 0.0043 (R490/R560). The new algorithm, obtained calibrating R560/R705 model, demonstrated an NRMSE of 17.8% in estimating Secchi disk depth in the Albufera of Valencia, compared to 20.7% for the previous one, indicating a significant improvement in algorithm performance and good accuracy in Secchi disk depth estimation in the Albufera of Valencia. Therefore, the new algorithm provides a more precise and reliable tool for estimating water clarity in the Albufera de Valencia using remote sensing data. This will contribute to better monitoring and management of water quality in this important aquatic ecosystem, valued for its natural and cultural heritage. Additionally, the results of this study highlight the importance of selecting appropriate optical models to estimate water clarity in highly turbid and eutrophic environments.