Abstract: Considering the effect of water flow on the transportation of Fe and Mn and describing its processes of redox,sorption,desorption,deposition and re-suspension in the reservoir,a joint 3-dimensional mathematical model for the hydrodynamics and the transportation of Fe and Mn was developed.The model simulated both horizontal and vertical gradients of Fe and Mn in Arha Reservoir.It was found that Fe and especially Mn stratify in accordance with the stratification of DO during summer.The redox cycles across the water sediment interface play a principal role in the rise of Fe and Mn concentrarions in the overlying water.It was also found that Fe and Mn loads from the tributaries have a carryover effect on the water quality through a secondary contamination in the reservoir.