Harmful algae blooms posing serious threats to the ecological environment occur frequently across the world. Multi-species algicidal bacteria were enriched by utilizing immobilized carriers in a pilot scale experiment, which significantly promoted the effect of algal control in the reactors. Under the optimal condition, the algicidal ratio and chlorophyll a degradation rate reached 87.69% and 47.00 μg/(L·d), respectively. The growth of Cyanophyta, diatom, Dinoflagellate and Cryptophyta was inhibited significantly by the joint action of algicidal bacteria and light shading of fillers, accounting for 53.74% and 36.47%, respectively. The results of 16S rRNA high-throughput sequencing suggested algicidal bacteria (10.17%) belonging to 13 genera were enriched. Among the algicidal process, Bacillus and Pseudomonas played crucial roles. Fluorescence spectroscopy and UV254 were adopted to assess the release of dissolved organic matter (DOM) and the precursors of disinfection by-products (DBPs). Two efficient algicidal strains (C1, C4) were isolated which showed high homology with Enterobacter asburiae JCM6051(T) and Pseudomonas simiae oli(T), respectively. This study provided new insights into the in-situ bioremediation of eutrophication in fresh water.