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Freshwater with high quality is crucial for both public health and aquatic biodiversity. However, freshwater resources face numerous challenges, including the proliferation of harmful algal blooms (HABs) caused by various cyanobacterial species that are generally triggered by human activities like agricultural runoff and wastewater. Native algicidal microbiomes may offer potential solutions, although challenges remain in utilizing microbial resources to mitigate HABs in freshwater environments. The combination of synthetic microbial community and probiotic development approaches with robust machine learning tools could allow us to harness native microbiomes to address water quality issues caused by HABs in large water bodies. A meta-analysis of around 100 research studies regarding algicidal bacteria-algae interactions was conducted to quantitatively assess the potential of taxonomically diverse microbial species in controlling HABs in freshwater ecosystems. Meta-analysis findings revealed that diverse species from common freshwater bacterial phyla such as Actinobacteria, Bacteroidota, Firmicutes, and Proteobacteria exhibited 50100 % algicidal activity against different algal species depending on interacting species and environmental conditions. Algicidal taxa (mainly against Microcystis aeruginosa) from both Actinobacteria and Firmicutes primarily included Actinomycetes and Bacillus species. However, Bacteroidota and alpha/beta Proteobacteria exhibited algicidal activity against a broader range of algal species, thus highlighting their potential for controlling multi-species HABs in freshwater environments. Based on this quantitative analysis, the current review puts forward synthetic microbial communities and machine-learning based frameworks to develop microbial solutions for protecting freshwater resources from HABs invasions.