The fractions of phosphorus (P) and Fe in the surface sediments of three typical urban shallow lakes (Xuanwu Lake, Daming Lake and Mouchou Lake) were determined using improved methods of SEDEX and BCR, respectively, and the relationship between P and Fe in sediments was also analyzed. P analyses showed that the relative lower content of Al-P was found in sediments of three urban lakes, while the percentage of Fe-P was in the range of 17.10%-27.88%, 16.68%-27.06% and 0.06%-0.17%, respectively, in Xuanwu Lake, Daming Lake and Mouchou Lake and the contents order was in line with the level of eutrophication. The contents of Ex-P, ACa-P and De-P were highest in Daming Lake while lowest in Mochou Lake. Ca-P was the main fraction, ranging from 32.51% to 75.39% in these lakes. Fe analyses showed that 69.17%-99.88% of Fe in sediments of three urban lakes was present in the residual fraction (F4), suggesting that F4 was the dominant fraction. While the contents of F1 and F2 in sediments of Xuanwu Lake were high, accounting for 6.46%-17.35%. It may be one of the main factors causing the frequent outbreak of cyanobacteria in Xuanwu Lake. There were significant negative correlations (p < 0.01) between TP and F1, F2 and F3, and the correlativity coefficient was - 0.95, - 0.94, - 0.81, respectively. Ex-P, Al-P and Or-P correlated significantly to F1 and F2, suggesting that Ex-P, Al-P and Or-P were sensitive to environment factors due to their active characteristics. ACa-P and De-P were bio-unavailable phosphorus, but they had significantly negative correlativity to F1, F2 and F3. Thus, further study should be performed on the reaction mechanism of ACa-P and De-P.