The sediment-bound organic phosphorus (Po) is increasingly recognized as a critical internal source for the lake eutrophication process due to its potential bioavailability for organisms. However, limited recognition about the bioavailability variations of sediment Po impeded the in-depth understanding upon the biogeochemical process of Po, especially the differences between high and low risk-periods of algal blooms (HRP-ABs and LRP-ABs). Primarily, significant difference between HRP-ABs (July–December) and LRP-ABs (January–June) was discerned by Mann-Kendall tests of TP, Chla and algal biomass. Biochemical and molecular characterizations, e.g., enzymatic hydrolysis with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS), were combined to discern the bioavailability variation of sequential extracted sediment Po in HRP-ABs and LRP-ABs. The contents of enzymatically hydrolysable Po decreased in the following order: NaOH-Po > NaHCO3-Po > H2O-Po. The concentrations of bioavailable Po, including labile phosphate monoester (Labile Mono-P) and phosphodiester (Diester-P) were 21.8–58.4 mg/kg (averagely 44.3 mg/kg) and 19.5–35.8 mg/kg (averagely 28.2 mg/kg) in HRP-ABs and LRP-ABs, respectively. Notably, the amounts of bioavailable H2O-Po and NaHCO3-Po in HRP-ABs (13.4–33.3 mg/kg) were nearly 2–3 times of that in LRP-ABs (3.9–14 mg/kg), while no significant NaOH-Po differences were observed. Similarly, contrasting the HRP-ABs with LRP-ABs, more P-containing formulas were assigned in H2O-Po (2526 vs 1884) and NaHCO3-Po (1554 vs 863), with similar abundance in NaOH-Po. Furthermore, the molecular composition of bioavailable Po (Bio-Po, H/C > 1.2 O/C > 0.5), especially Bio-Po containing two P atoms (Bio-2Po) displayed significant variation in H2O-Po (308 vs 391, 217 vs 316) and NaHCO3-Po (114 vs 208, 40 vs 145) between HRP-ABs and LRP-ABs. This was largely attributed to its high bioavailability in Bio-2Po (>50% lipids, proteins and carbohydrates-like). Our findings upon the internally activated accumulation and transformation process interpretation of sediment bioavailable Po are of great significance for lake eutrophication control.