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The internal loading of P is reported to be the main factor initiating algal blooms. However, there are only a few reports on the dynamic variation of labile P in the sediment and overlying water during the decomposition of algal. In addition, the widely perceived relationship between labile P and Fe was not supported by in situ obtained values in freshwater. Consequently, the in situ simultaneous measurement of diffusion gradients in thin-film techniques (DGT) was applied on a large scale to detect the mechanisms of labile P and Fe in a typical shallow lake (Lake Hongze). The newly developed ZrO-DGT and ZrO-Chelex DGT were combined to obtain the concentration of labile P and Fe. Results showed that decomposition of algal might be the main contributor for the concentration dots and peaks of labile P in sediment profiles, as well as for the high values on the horizontal heterogeneity index of labile P at the depth of 0–30 mm of the sediment. Moreover, there existed significant difference between the apparent diffusion fluxes of labile P and Fe across the sediment–water interface which obtained from June sampling and October sampling. The results of apparent diffusion flux in two periods indicated the sediments changed from “sink” to “source” for labile P, especially at Sites 4–8, 10, 13–14, and 18. However, the role of the labile Fe has no significantly variation in the values of the diffusion flux. This phenomenon also contributed to the poor relationship between labile P and Fe in the sediment which obtained from the October sampling. Accordingly, we conclude that algal decomposition might be essential for internal loading of P in this aquatic ecosystem, and that also be the reason for vicious circle of algal occurrence in the following year in the center of Lake Hongze. [ABSTRACT FROM AUTHOR]