Transmission electron microscopy (TEM), soft X-ray scanning transmission X-ray microscopy (STXM), and μ-FTIR spectromicroscopy were used to map colloidal/particulate material in an ultra-oligotrophic lake, Lake Brienz, Switzerland, with a special focus on organic functionality. Within the statistical margin of error and the uncertainties arising from the representativeness of the results, the research reveals that organic material was associated with potassium-rich inorganic colloids present in surface and deep water (depths of 1 and 100 m, respectively), which indicates a vertical transfer of aggregates by sedimentation. Pure organic colloids could only be detected in surface waters. In addition, correlation map analysis of synchrotron-based μ-FTIR and carbon K-edge STXM spectromicroscopic data using spectra from the Lütschine and Aare Rivers as target spectra revealed spectral similarities with organic components from both tributary rivers in deeper regions (100 m) of the lake. The results prove that STXM and μ-FTIR can characterize colloidal and particulate organic material in low organic carbon systems.