Background and aims <p>Organic P (P_o) plays a crucial role in P cycle of lake ecosystems. However, source identification of P_o in lake basins was still bewildering due to the diversity of P occurrence.</p> Methods <p>We conducted a study to analyze P_o in sediments from lake, estuaries and ponds with agricultural soils surrounding Shijiuhu Lake in the lower reaches of the Yangtze River Basin, China. The methods encompassed sequential P_o fractionations, solution ³¹P NMR spectroscopy, and enzymatic parameters including alkaline phosphatase activity (APA).</p> Results and discussion <p>Compare to lake sediments, agricultural soils had higher proportion of humic acid-bound P_o (HA-P_o, means: 37.8% vs. 41.7%) and less phosphodiester (diester-P_o, 0.44–2.53% vs.6.94–13.4%). Mean APA values decreased as follows: soil &gt; lake &gt; estuary &gt; pond. P_o in lake sediments dominated by HA-P_o and resistant P_o (Res-P_o) with the highest proportions of phosphate monoesters (Mono-P_o) and diester-P_o among various land-use types. Pond sediments exhibited dominant macromolecules. P_o in estuary sediments was mainly composed of FA-P_o (14.5–34.1%).</p> <p>The results indicated that the presence of high P_o in lake sediments was attributed to algal contributions together with external inputs. Agricultural soils input predominantly contribute to P_o in some lake sediments. Otherwise, estuary sediments accumulated P_o originating from farmland and ponds, contributed crucially to the lake ecosystem.</p> Conclusion <p>These results proved the predominantly contribution of agricultural soils to lake sediments and emphasized the mechanisms governing P_o cycling in estuaries connected with lakes. This finding is crucial for effective management strategies targeting P loads within the lake ecosystem.</p>