The investigation of soil and aquatic organic matter samples by synchrotron-based scanning transmission X‑ray microscopy and C‑1s NEXAFS spectroscopy is presented. The organic chemistry of these environmental samples was investigated at different scales with regards to spatial and seasonal variations. This work demonstrated that heterogeneity in soil organic matter particles occurs within different scales. For the first time it could be shown, that water-dispersible colloidal particles exhibit significant variations in their functional group content within the scale of single particles as well as between particles derived from different horizons. The use of X‑ray microscopy opened up the possibility to visualize and quantify these differences in functional group chemistry within particles at atmospheric conditions and provided insight into the complex reactions that occur in environmental ecosystems.