“Sargassum” is a pelagic species of algae that drifts and aggregates in the tropical Atlantic Ocean. The number of Sargassum aggregations increased in the Caribbean Sea during the last decade. The aggregations eventually wash up on shores thus leading to a socio-economic issue for the population and the coastal ecosystem. Satellite ocean color data, such as those provided by the Sentinel-3/OLCI satellite sensor (Copernicus), can be used to detect the occurrences of Sargassum and to estimate their abundance per pixel using the Maximum Chlorophyll Index (noted MCI). Such an index is, however, ineffective if the algae are located beneath the sea surface, which frequently happens, considering the rough Caribbean oceanic waters. The objective of this study is to propose a relevant methodology that enables the detection of underwater Sargassum aggregations. The methodology relies on the inversion of the radiative transfer equation in the water column. The inverted model provides the immersion depth of the Sargassum aggregations (per pixel) and their fractional coverage from the above water reflectances. The overall methodology has been applied to Sentinel-3/OLCI data. The comparison with the MCI method, which is solely devoted to the sea surface retrieval of Sargassum aggregations, shows that the proposed methodology allows retrieving about twice more Sargassum aggregation occurrences than the MCI estimates. A relative increase of 31% of the fractional coverage over the entire study area is observed when using the proposed method in comparison to MCI method. For the satellite scenes considered here, the rate of Sargassum aggregations immersed between 2 m and 5 m depth ranges between 30% and 51% over the total amount (i.e., surface + in-water), which clearly demonstrates the importance of considering the retrieval of in-water aggregations to gain understanding on Sargassum spatial variability in the oceanic and coastal ecosystems.