Inland waters are very sensitive ecosystems that are mainly affected by pressures and impacts within their watersheds. One of water’s dominant constituents is the suspended particulate matter that affects the optical properties of water bodies and can be detected from remote sensors. It is important to know their composition since the ecological role they play in water bodies depends on whether they are mostly organic compounds (phytoplankton, decomposition of plant matter, etc.) or inorganic compounds (silt, clay, etc.). Nowadays, the European Space Agency Sentinel-2 mission has outstanding characteristics for measuring inland waters’ biophysical variables. This work developed algorithms that can estimate the total concentration of suspended matter (TSM), differentiating organic from inorganic fractions, through the combined use of Sentinel-2 images with an extensive database obtained from reservoirs, lakes and marshes within eastern zones of the Iberian Peninsula. For this, information from 121 georeferenced samples collected throughout 40 field campaigns over a 4-year period was used. All possible two-band combinations were obtained and correlated with the biophysical variables by fitting linear regression between the field data and bands combination. The results determined that only using bands 705 or 783 lead to the obtaining the amount of total suspended matter and their organic and inorganic fractions, with errors of 10.3%, 14.8% and 12.2%, respectively. Therefore, remote sensing provides information about total suspended matter dynamics and characteristics as well as its spatial and temporal variation, which would help to study its causes.