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Suspended matter (SM) from the Nyong basin (Cameroon, Africa), a tropical watershed, was collected by tangential flow ultrafiltration to separate particulate (>0.45 μm) and colloidal ( 20 kDa) fractions. In this basin, two distinctive systems in a selected small catchment (Nsimi–Zoetele) of the Nyong river basin have been considered: (i) colourless water (groundwater and spring) with a low suspended load ( 10 mg/l) and contains higher amounts of SM (10–20 mg/l) than the colourless water. Freeze-dried samples of SM have been analysed by X-ray diffraction (XRD), transmission electron microscopy (TEM), Fourier-transform infrared spectroscopy (FTIR), electron paramagnetic resonance spectroscopy (EPR), and visible diffuse reflectance spectroscopy (DRS). Colourless water mainly contains mineral phases, such as poorly ordered kaolinite, plus quartz and goethite in the particulate fraction, and euhedral kaolinite plus amorphous iron oxyhydroxides in the colloidal fraction. In contrast, the SM in coloured water is mainly organic in nature. The mineral phases in the particulate fraction are similar to those from clear water, but with additional phytoliths and diatom frustules composed of biogenic opal. In the colloidal fraction, complexation of Fe3+ and Mn2+ with organic matter is evidenced by EPR, together with significant occurrence of Fe oxyhydroxides associated with organic matter. The sites of Al, Si, Fe, Mn in colloidal fractions derived from spectroscopic analyses are discussed with reference to chemical analyses performed by inductively coupled plasma mass spectrometry. Most of the observed solid phases or species correspond to those expected from published thermodynamic calculations for the same hydrosystem, except the colloidal iron oxyhydroxides in the coloured water. The presence of such iron phases is emphasised since they are expected to have large sorption capacities for numerous trace elements. The crystal chemistry of SM is used to discuss the origin of the mineral particles transported from the soil to the main rivers in terms of mechanical and chemical erosion processes.