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Abstract Suspended particulate matter (SPM) is generally divided into inorganic (SPIM) and organic (SPOM) parts; they come from different sources, and have different impacts on the optical properties and/or water quality of lake. However, in a specific remote sensing process, they are not retrieved separately. Using in-situ data of 59 lakes along the middle and lower reaches of the Yangtze River (MLR-YR) in dry season (April) and wet season (August) in 2012, we first studied the absorption properties and sources of different SPM. On this basis, we proposed a workflow for simultaneously estimating SPIM and SPOM from satellite data. Our results are as follows: Bio-optical compositions of SPM in these eutrophic shallow lakes tempo-spatially varied greatly and were dominated by human-induced eutrophication. Phytoplankton contributed 18.42 ± 18.92% of SPIM and 26.22 ± 19.24% of SPOM in April 2012, but 30.4 ± 23.41% of SPIM and 47.03 ± 18.1% of SPOM in August 2012. The trophic state index explained 42.84% of SPOM variation in April 2012, and 54.64% in August 2012. Moreover, there were strong linear relationships between SPIM concentration and non-algal particle absorption coefficient (Pearson's r = 0.73 ; p < 0.01) and between SPOM concentration and phytoplankton absorption coefficient (r = 0.76 ; p < 0.01). Based on these results, SPIM and SPOM concentrations in the lakes along the MLR-YR could be retrieved from OLCI/Sentinel-3A satellite data, respectively. This study has a great significance for real-time monitoring and managing aquatic environment in various eutrophic and/or shallow lakes as a group. Graphical abstract Unlabelled Image Highlights • Lakes along the middle and lower reaches of Yangtze River were seriously eutrophic. • Suspended particle compositions were dominated by human-induced eutrophication. • Bio-optical compositions of suspended particles differed by trophic state index. • Monitoring suspended particle compositions using satellite data was achievable. [ABSTRACT FROM AUTHOR]