Towards Reliable High-Resolution Satellite Products for the Monitoring of Chlorophyll-a and Suspended Particulate Matter in Optically Shallow Coastal Lagoons

Coastal lagoons are fragile and dynamic ecosystems that are particularly vulnerable to climate change and anthropogenic pressures such as urbanization and eutrophication. These vulnerabilities highlight the need for frequent and spatially extensive monitoring of water quality (WQ). While satellite remote sensing offers a valuable tool to support this effort, the optical complexity and shallow depths of lagoons pose major challenges for retrieving water column biogeochemical parameters such as chlorophyll-a ([chl-a]) and suspended particulate matter ([SPM]) concentrations. In this study, we develop and evaluate a robust satellite-based processing chain using Sentinel-2 MSI imagery over two French Mediterranean lagoon systems (Berre and Thau), supported by extensive in situ radiometric and biogeochemical datasets. Our approach includes the following: (i) a comparative assessment of six atmospheric correction (AC) processors, (ii) the development of an Optically Shallow Water Probability Algorithm (OSWPA), a new semi-empirical algorithm to estimate the probability of bottom contamination (BC), and (iii) the evaluation of several [chl-a] and [SPM] inversion algorithms. Results show that the Sen2Cor AC processor combined with a near-infrared similarity correction (NIR-SC) yields relative errors below 30% across all bands for retrieving remote-sensing reflectance R_rs(λ). OSWPA provides a spatially continuous and physically consistent alternative to binary BC masks. A new [chl-a] algorithm based on a near-infrared/blue R_rs ratio improves the retrieval accuracy while the 705 nm band appears to be the most suitable for retrieving [SPM] in optically shallow lagoons. This processing chain enables high-resolution WQ monitoring of two coastal lagoon systems and supports future large-scale assessments of ecological trends under increasing climate and anthropogenic stress.