A mechanistic model was developed to simulate one-dimensional pesticide transport in two-stage vertical flow constructed wetland. The two pesticides taken under study were carbendazim and chlorothalonil. The water flow patterns within the constructed wetland were simulated using the Richards equation. Water content and vertical flux, which are the outputs of the substrate water flow model, were used to calculate the substrate moisture-related parameters and advection term in the solute transport model. The governing solute transport equation took into account a total of six processes: advection, molecular diffusion, dispersion, adsorption to the solid surface, degradation and volatilization. A total of 14 simulation cases, corresponding with available experimental data, were used to calibrate the model, followed by further simulations with standardized influent pesticide concentrations. The simulations indicated that the constructed wetland reached a steady state of pesticide removal after 7 days of operation. Two distinct water flow patterns emerged under saturated and unsaturated conditions. The patterns observed while varying the hydraulic loading rates were similar for each individual saturation condition. Two-factor ANOVA of the simulated data further revealed that the carbendazim and chlorothalonil removal was dependent on the hydraulic loading rates, but it was independent of the influent pesticide concentration. Analysis of the simulated pesticide removal showed that degradation emerged as the predominant removal process over time for both the pesticides. The model developed in this study can be an important tool for the design and construction of treatment wetlands for pesticide removal from wastewater.