In order to clarify the transport dynamics and ecological risks of pesticides in ditches and ponds, this paper presenteda pesticide transport model based on a monitoring study on drainage process and pesticide concentrations in field ditches (FD) in a small agricultural watershed in Yangzhou of Jiangsu Province, China. With the proposed model, we analyzed the spatial and temporal variations of chlorpyrifos (CPF) from FD to main ditches (MD) and ponds (PD) under different drainage flow and concentrationconditions, and evaluated the ecological risks of the CPF to aquatic animals. The monitoring results showed that peak drainage flow did not synchronize with peak pesticide concentrations in FD, the pesticide loading process was either with low flow and high concentration or high flow and low concentration. The model predictions of CPF transport process showed that ditches and ponds had a significant buffering effect on pesticide loading pulses, thus reducing peak concentrations of pesticide in drainage discharge. In the low-flow and high-concentration event, the observed peak concentration of CPF was as high as 330μg/L in FD, but reduced to 0.05μg/Lin MD and 0.00002μg/L in PD, resulting in reductions of 99.98% and 100% in MD and PD, respectively. In the high-flow and low-concentration event, the peak concentration of CPF was 2.5μg/L in FD, 0.02μg/L in MD, and 0.0006μg/L in PD, resulting in reductions of 99.2% and 99.98% in MD and PD, respectively. These results showed supportive effect of high-flow process on the output process. Under both types of drainage flow events, CPF concentrations were at low levels in MD (<0.1μg/L) and PD (<0.001μg/L),posing relatively low ecological risks to 16species of aquatic animal species that might be present in the ditches and ponds, except one species with a medium to high risk. Under a hypothetical unfavorable combination of synchronized high flow and high concentration event, the calculated peak concentrations of CPF was 2.55μg/Lin MD and 0.039μg/L in PD, making the number of aquatic animals with high ecological risk rise to 6species, regardless of the great reductions of 99.2% and 99.99% in MD and PD, respectively. Findings from this research may provide a scientific basis for pesticide pollution control and aquatic environmental protection in similar regions.