Natural landscape water and substrate were taken to simulate the release of substrate pollutants in micropolluted water bodies, and a calcium silicate- sodium alginate (CS-SA) bioremediation system was constructed. The removal of ammonium nitrogen (NH4+-N), total nitrogen (TN) and Phosphate (PO43--P) were 99.14 %, 98.90 % and 84.44 %, respectively. The Ca2+ continuously released by CS-SA provided good microbial-induced calcium precipitation (MICP) conditions for Acinetobacter calcoaceticus strain HM12, and the removal efficiency of both Zn2+ and Cd2+ was 100 %, and the pH after remediation was consistent with that of natural water bodies. NH4+-N was removed by heterotrophic nitrification- aerobic denitrification (HN-AD) of strain HM12, and heavy metals and phosphorus were removed by co-precipitation and adsorption by MICP. High-throughput sequencing results showed that strain HM12 was effective as a bioinoculant for the remediation of the aquatic environment. The construction and operation of this bioremediation system provided a method for micropolluted water treatment and recovery of phosphorus and heavy metals.