Biocrust-mediated in situ bioremediation could be an alternative strategy to mitigate metal(loid) pollution in aquatic habitats. To better understand the roles of biocrusts in regulating the fate of metal(loid)s, we examined the morphology, composition and structure of biological aqua crusts (BAC) developed in the mine drainage of a representative Pb/Zn tailing pond, and tested their effectiveness for immobilizing typical metal(loid)s. Unlike terrestrial biocrusts, BAC results from an assembly of compounds produced by the strong microbial activity and mineral compounds present in the aquatic environment. The BAC exhibited a unique flexible, spongy and porous structure with a specific surface area of 12-22 m2 g−1, and was able to effectively concentrate various metal(loid)s (e.g. Cd, 0.26-0.60 g kg−1; Pb, 0.52-0.66 g kg−1; As, 10.4-24.3 g kg−1). The concentrations of metal(loid)s (e.g. Cd and As) in the BAC were even three to seven times higher than those in the source tailings, and more than 98% of immobilized metal(loid)s were present as the highly stable non-EDTA-exchangeable fraction. Adsorption on the well distributed micro-particles of the clay minerals (e.g. kaolinite) and the organic matters (2.0-2.7 wt.%) were found to be the major mechanisms for BAC to bind metal cations, whereas adsorption and coprecipitation on Fe/Mn oxide (e.g. FeOOH), was proposed to be the dominant pathway for accumulating metal(loid)s, especially As. The decrease in aqueous concentrations of the metal(loid)s along the drainage could be attributed in part to the scavenging effects of the BAC. These findings therefore provide new insights into the possible and efficient strategy for metal(loid) removal from water bodies, and highlighted the important role of BAC as a nature-based solution to benefit the bioremediation of mining area.