The characteristic of water transport and loss in a direct-seeded paddy field, Danyang Region at upstream of Taihu Lake Basin, was studied under local traditional field water management using Hydrus-1D model. Results show that the drying/wetting boundary condition on soil surface was well simulated by using divided stress period method in the Hydrus-1D model, and the estimated hydrodynamic parameters can be applied to simulate water movement in a direct-seeded paddy field. The water loss from the experimental paddy field occurred mainly through both surface runoff during early stage of rice growing season and leakage, which accounted for about 21.7% and 12.2% (at soil depth of 60 cm) of the total input water (precipitation and irrigation water), respectively. The surface runoff caused little except for both during the intense rainfall and the soil-drying stage. The fertilization should be paid more attention during early stage of rice growing season and just after soil-drying stage, when the major surface runoff and leakage of water caused, which maybe lead to a mass of nutrient loss.