MARTHE (Modelling Aquifers with an irregular Rectangular grid, Transport, Hydrodynamics and Exchanges) is a versatile 3D groundwater model designed to enable the hydrodynamic and hydrodispersive modelling of groundwater flow in hydrosystems. Refinements to the model were made as part of the European project PEGASE to allow the simulation of pesticide fate in the soil. New descriptions for cropping and pesticide sorption and degradation were added to the model. The verification exercise undertaken using analytical solutions published in the literature (sorption, degradation) and experimental data (cropping, degradation) demonstrated that the new code added to MARTHE has been correctly implemented in the model. In addition, the close fits obtained between predicted and theoretical/measured data confirmed the sound numerical schemes of the model. These refinements and their testing mean that the model can now be used with confidence to simulate the fate of pesticides from the soil surface to and in the groundwater. The model is expected to be a useful tool in the modelling of pesticide fate through the whole continuum root zone - unsaturated zone - saturated zone, in 1, 2 or 3 dimensions. In particular, the model may be used to i) assess the risk of pesticide leaching to groundwater resources at a range of scales; ii) provide explanations for detection / non-detection of pesticides in monitoring programs; and, iii) manage inputs of pesticide to a particular area within a context of sustainability of groundwater resources.