The Water Cleanser™ bio-wax is a novel biomaterial that can enhance the activity and quantity of microorganisms, which possesses a microporous architecture with sustained-release microbial enhancers, demonstrating capacity to activate metabolic pathways for indigenous aquatic microbiota proliferation. Notwithstanding this functional characteristic, the operational efficacy variance and underlying mechanisms remain indeterminate given the ecological heterogeneity in microbial consortia composition, nutrient bioavailability (particularly C:N:P stoichiometry), and trophic status across natural aquatic systems. Through tri-monthly controlled mesocosm experiments, this investigation systematically evaluated matrix-mediated biogeochemical processes including denitrification efficiency, phosphorus sequestration dynamics, and cyanobacterial bloom suppression under varying nutrient regimes. Experimental data revealed that within total nitrogen (TN) concentrations of 0.2–2.0 mg/L and total phosphorus (TP) levels of 0.2–0.4 mg/L, the microbial carrying capacity exhibited 54.5% enhancement concomitant with increasing initial N/P loading. Correspondingly, matrix-amended systems achieved significant pollutant removal increments: TN (14.8%), NH₃-N (10.8%), and COD (12.9%) relative to baseline conditions. Cyanobacterial biomass suppression reached 32.5–55.6% compared to control cohorts, though inhibitory efficacy inversely correlated with N/P gradients (23.1% attenuation per trophic state elevation). The bio-wax enhanced the activity and biomass of heterotrophic bacterial species such as Bacillus thuringiensis and Bacillus cereus in aquatic environments. These microorganisms rapidly grow and proliferate by consuming nutrients (e.g., nitrogen, phosphorus) and organic matter from their surroundings. As the N/P loading increases, the water purification efficiency of the bio-wax was correspondingly enhanced, thereby suppressing cyanobacterial biomass. These findings establish nutrient-biota interactions mediated by bioremediation matrices, providing critical parameters for optimizing eutrophication mitigation strategies in lacustrine ecosystems.