Harmful algal blooms (HABs) dominated by toxigenic cyanobacteria represent a growing threat to freshwater ecosystems and drinking water security. While phosphorus is widely recognized as a key driver of cyanobacterial proliferation, the ecological roles of naturally derived nutrient sources remain poorly understood. In this study, field-based mesocosm experiments were conducted to compare the effects of various nutrient sources originating from both autochthonous and allochthonous origins—sediments, cyanobacterial scums, benthic periphyton mats, and agricultural soils—on cyanobacterial and <i>Microcystis</i> growth, as well as microcystin (MC) production. All nutrient treatments were adjusted to a uniform total phosphorus concentration (0.4 mg/L), and nitrogen limitation was excluded. Cyanobacterial biomass, assessed via chlorophyll-a and phycocyanin fluorescence, was consistently higher in all nutrient-amended mesocosms than in the inorganic phosphorus control. Notably, periphyton mat extracts promoted sustained biomass accumulation during the latter incubation stages. MC concentrations were elevated in all nutrient-amended treatments relative to the control, although no significant differences were observed among the various nutrient sources. Quantitative PCR analysis revealed that while total <i>Microcystis</i> abundance did not differ significantly across treatments, the abundance and relative proportion of toxigenic <i>Microcystis</i> (<i>mcyA</i> gene) were significantly higher in periphyton mat–amended mesocosms. In contrast, MC production normalized to toxigenic cell abundance showed no significant variation among treatments, indicating that strain-specific traits exert a stronger influence on toxin production than the nutrient source type. These findings demonstrate that organically derived nutrient sources, particularly periphyton mats, play a critical role in sustaining HABs and selectively promoting toxigenic strains. Consequently, effective HAB mitigation strategies should extend beyond simple total phosphorus reduction to include the management of internal nutrient sources and phosphorus speciation within aquatic systems.