Combining organic carbon (OC) measurements with the classic MBTH (3-methyl-2-benzothiazolinone hydrochloride) method for carbohydrate determination and a new voltammetric method for the determination of refractory organic matter (ROM) made it possible, for the first time, to quantify the types, sources and fate of submicron organic matter present in an ultra-oligotrophic lake (Lake Brienz, Switzerland). The lake is extremely rich in suspended glacial flour in summer (glacier melting season). Measurements were taken from June 2004 to October 2005 from 1.2 μm filtered samples. OC concentration remained extremely low throughout the year (below 1 mg C L−1). MBTH carbohydrate concentration was very low in the lake (0.06–0.43 mg C L−1) and in the two tributary rivers (0.06–0.25 mg C L−1). Lake carbohydrate concentration only correlated with phytoplanktonic biomass at the onset of the productivity period. The results suggest that differences in MBTH concentration may sometimes reflect differences in the nature of the carbohydrates rather than differences in carbon concentration. Extensive fibril formation was evidenced by transmission electron microscopy (TEM) observations. ROM concentration in the lake was also very low (0.1–0.2 mg C L−1). Significant variation in ROM riverine input was due to either annual occurrences (snow melting) or irregular episodes (floods). Melting snow was responsible for about 30% of the lake's annual ROM input. One box mass balance calculations showed that about 25% of ROM was lost within the lake. Evidence gleaned from TEM and STXM (scanning transmission X-ray microscopy) observations clearly indicates that this is mainly caused by ROM sedimentation after association with inorganic colloids.