A new coupled model (PCPFSWMS) was developed for simulating fate and behavior of pollutant in paddy water and paddy soil. The model coupled the PCPF-1, a lumped model simulating pesticide concentrations in paddy water and 1 cm-surface sediment compartment, and the SWMS-2D, a finite element numerical model solving Richard's and advection-dispersion equations for solute transport in soil compartment. The coupling involved improvements on interactions of the water flow and the concentration the pollutant of at the soil interface between both compartments. The monitoring data collected from experimental plots in Tsukuba, Japan in 1998 and 1999 were used to parameterise and calibrate hydraulic functioning, hydrodynamic and hydrodispersive parameters of the paddy soil. The analysis on the hydraulic functioning of paddy soil revealed that the hard pan layer was the key factor controlling percolation rate and tracer transport. Matric potential and tracer monitoring highlighted the evolution of saturated hydraulic conductivity (KS) of hard pan layer during the crop season. KS slightly decreased after puddling by clay clogging and strongly increased after mid term drainage by drying cracks. The model was able to calculate residential time in every soil layers. Residential time of tracer in top saturated layers was evaluated to be less than 40 days. It took 60 days to reach the unsaturated layers below hardpan layer.