The adsorption of Zn2+ ions onto biogenic elemental selenium nanoparticles (BioSeNPs) was investigated. BioSeNPs were produced by reduction of selenite (SeO32−) in the presence of anaerobic granules from a full scale upflow anaerobic sludge blanket (UASB) reactor treating paper mill wastewater. The BioSeNPs have an iso-electric point at pH 3.8 at 5 mM background electrolyte concentration. X-ray photoelectron spectroscopy showed the presence of a layer of extracellular polymeric substances on the surface of BioSeNPs providing colloidal stability. Batch adsorption experiments showed that the uptake of Zn2+ ions by BioSeNPs was fast and occurred at a pH as low as 3.9. The maximum adsorption capacity observed was 60 mg of zinc adsorbed per g of BioSeNPs. The Zn2+ ions adsorption on the BioSeNPs was largely unaffected by the presence of Na+ and Mg2+, but was impacted by the presence of Ca2+ and Fe2+ ions. The colloidal stability of BioSeNPs decreased with the increasing Zn2+ ions loading on BioSeNPs (increase in mg of zinc adsorbed per g of BioSeNPs), corresponding to the neutralization of the negative surface charge of the BioSeNPs, suggesting gravity settling as a technique for solid-liquid separation after adsorption. This study proposes a novel technology for removal of divalent cationic heavy metals by their adsorption on the BioSeNPs present in the effluent of an UASB reactor treating selenium oxyanions containing wastewaters.