Microbial selenium (Se) bioremediation is based on conversion of water soluble, toxic Se oxyanions to water insoluble, elemental Se. Formed biogenic elemental Se is of nanometer size, hampering straightforward separation from the aqueous phase. This study represents the first systematic investigation on colloidal properties of pure biogenic Se suspensions, linking electrophoretic mobility (ζ-potential) to column settling behavior. It was demonstrated that circumneutral pH, commonly applied in bioremediation, is not appropriate for gravitational separation due to the negative ζ-potential preventing agglomeration. Mono/di/trivalent counter cations and acidity (protons) were used to screen efficiently the intrinsic negative charge of biogenic Se suspensions at circumneutral pH. Fast settling was induced by La(3+) addition in the micromolar range (86.2 ± 3.5% within 0.5 h), whereas considerably higher concentrations were needed when Ca(2+) or Na(+) was used. Colloidal stability was furthermore studied in different model waters. It was demonstrated that surface waters as such represent a fragile system regarding colloidal stability of biogenic Se suspensions (ζ-potential ∼ -30 mV), whereas dissolved organic matter increases colloidal stability. In marine waters, biogenic Se is colloidally destabilized and is thus expected to settle, representing a potential sink for Se during transport in the aquatic environment.