This study investigated the growth dynamics and microcystin (MC) production of Microcystis in response to various autochthonous and allochthonous nutrient sources, specifically cyanobacterial scum, floating periphyton mats, sediment, and agricultural soil. Chemical analysis revealed that cyanobacterial scum is a major nitrogen reservoir (25.72 mg/g of dry weight(g dw)), while periphyton mats serve as significant phosphorus buffers through luxury uptake (1.92 mg/g dw). Laboratory cultures of <i>Microcystis</i> strains NIER10004 and CBE51 demonstrated that sediment extracts promoted the highest growth rates (0.0160 and 0.0166 OD750/d, respectively) and the greatest biomass-to-total phosphorus ratios. Phosphorus uptake followed a biphasic pattern: a rapid depletion of orthophosphate in the first 10 days, followed by a transition to organic phosphorus utilization, likely facilitated by alkaline phosphatase activity. MC concentrations peaked at the onset of the stationary phase, though total MC content showed a low correlation with the specific nutrient source, suggesting that nutrient supply primarily drives biomass expansion rather than MC biosynthesis rates. Given the feasibility of mechanical removal, artificial harvesting of periphyton mats during spring—when increased microbial activity in sediments causes the mats to detach and float—is proposed as a more viable and cost-effective management strategy than expensive sediment dredging for mitigating harmful algal blooms in eutrophic reservoirs.