Ongoing rapid arctic warming leads to extensive permafrost thaw, which in turn increases the hydrologic connectivity of the landscape by opening up subsurface flow paths. Suspended particulate organic matter (POM) has proven useful to trace permafrost thaw signals in arctic rivers, which may experience higher organic matter loads in the future due to expansion and increasing intensity of thaw processes such as thermokarst and river bank erosion. Here we focus on the Kolyma River watershed in Northeast Siberia, the world's largest watershed entirely underlain by continuous permafrost. To evaluate and characterize the present‐day fluvial release of POM from permafrost thaw, we collected water samples every 4–7 days during the 4‐month open water season in 2013 and 2015 from the lower Kolyma River mainstem and from a small nearby headwater stream (Y3) draining an area completely underlain by Yedoma permafrost (Pleistocene ice‐ and organic‐rich deposits). Concentrations of particulate organic carbon generally followed the hydrograph with the highest concentrations during the spring flood in late May/early June. For the Kolyma River, concentrations of dissolved organic carbon showed a similar behavior, in contrast to the headwater stream, where dissolved organic carbon values were generally higher and particulate organic carbon concentrations lower than for Kolyma. Carbon isotope analysis (δ13C, Δ14C) suggested Kolyma‐POM to stem from both contemporary and older permafrost sources, while Y3‐POM was more strongly influenced by in‐stream production and recent vegetation. Lipid biomarker concentrations (high‐molecular‐weight n‐alkanoic acids and n‐alkanes) did not display clear seasonal patterns, yet implied Y3‐POM to be more degraded than Kolyma‐POM.