Sediment water-extractable organic phosphorus (WEOP) is an important potential available P source in lake systems. However, its characteristics and composition remain largely unknown, which limits the effectiveness of internal P loading control. Here, we used Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) to characterize the chemical and molecular composition of WEOP. A total of 75–670P-containing molecular formulas (CHOP) were detected in 12 sediment samples (3% of total formulas). Higher ratio of O atoms in the WEOP formulas was found to be associated with lower proportion of C and H atoms and higher molecular weight compounds. WEOP formulas were predominantly comprised of compounds with one and two P atoms. Statistical analysis suggested that carbon-hydrogen bond groups and oxidized phosphorus functional groups were the dominant intrinsic drivers for the formula diversity of compounds with one and two P atoms, respectively. For WEOP composition, most of the P elements were incorporated into aliphatic compounds (average 29.0%), lipids (27.6%), and lignin (21.6%), with fewer into carbohydrates (8.8%), unsaturated hydrocarbons (8.4%), tannins (3.0%), and condensed aromatic structures (1.6%). Analysis of controlling factors showed that anthropogenic activities and water-extractable organic matter (WEOM) determined the WEOP molecular characteristics and composition. The decreasing order regarding the molecular diversity of WEOP sources as: livestock and poultry manure > WWTP effluent ≈ agricultural nonpoint sources > autochthonous origin. Anthropogenic activity intensity was positively correlated with WEOP molecular diversity and lignin-type components. Terrigenous WEOM with higher humification expanded WEOP molecular diversity, whereas fresh endogenous WEOM with higher humification reduced its molecular diversity. In general, WEOP was bioavailable and easily biodegradable in sediment, since it was predominantly comprised of compounds with H/C > 1.5 (65.5%).