Predicting pollutant transport in coastal ecosystems has become an important topic in many industrial and environmental projects, because of the degradation of water quality and conflicts related to multiple use of coastal resources. Most numerical studies on coastal catchment do not consider flow and pollutant fluxes through wetlands, or simulates theses transfers using “black box” based on linear regressions that greatly simplifies the complexity of the underlying processes. This paper presents a numerical study on the simulation of pesticide transport and degradation in the artificial wetland drainage channels of the Breton-Vendéen marsh (west coast of France). The one-dimensional (1-D), open source MASCARET modelling tool is used. The 1-D unsteady water flow through a network of open channels is represented by the shallow water equations. The water quality module of MASCARET simulates solute transport processes, consisting of advection, dispersion and mass reduction/generation by physical, chemical and biological mechanisms. Results show that the 1-D model is a reliable tool for simulating pollutant transfer through the coastal wetlands drainage channels. Moreover, it is possible to link landward and seaward models to MASCARET, which allows simulating water and pollutant propagation from watershed to coastal sea through wetland drainage channels with a high level of confidence