Sequential extraction was used to study the historical dynamics and fluxes of the chemical fractions of manganese (Mn) in sediments collected from the Pearl River Estuary (PRE), southern China. Results revealed that the proportion of Mn associated with different fractions decreased in the order of acid-soluble fraction (F1) > reducible fraction (F2) > residual fraction (F4) > oxidizable fraction (F3). F1 (47%) was the dominant Mn fraction, indicating the strong bioavailability of Mn to aquatic organisms in the PRE. In addition, the Mn fraction F2 was present at an average rate of 27.93 % in surface sediments, indicating that it could be mobilized when environmental conditions become increasingly reducing or oxidizing. The decline in Mn fraction fluxes after 2006 indicated that the region has partially decreased due to the removal of heavily polluting industries and effective control of sewage discharge.