Wet chemical methods such as sequential extraction procedures are commonly used to assess selenium fractionation in anoxic environments, allowing an estimation of the mobility and bioavailability of selenium. However, the interpretation can be biased by unselective extraction of targeted species and artifacts introduced during the extraction. Here, the selectivity of the single extraction steps to gain reliable selenium speciation information are scrutinized for the first time by direct, nondestructive X-ray absorption near edge structure (XANES) spectroscopy at the selenium K-edge. The sequential extraction procedures seriously overestimated the elemental selenium fraction, as major parts (58%) of the total selenium were present as metal selenides and organic selenium compounds, although extracted in the elemental fraction. Spectral fitting of the XANES spectra by the least-squares linear combinations utilizing a large set of model compounds, including previously neglected Se(-I) selenides, showed a novel degree of complexity in the speciation of selenium treating anaerobic biofilms, with up to 4 modeled selenium species contributing to the speciation, i.e., different elemental, organic, and metal-bound selenium species. Furthermore, a short exposure (10 min) to ambient air during the sequential extraction procedure induced the oxidation of organic selenium compounds, revealing the fragility of selenium speciation in anaerobic biofilms.