A sensitivity analysis of the HYDRUS-1D model was performed based on scenarios that represented the fate of a nonvolatile pesticide in three soils. We used the latest dual-porosity, transient mobile–immobile (MIM) version of HYDRUS-1D that includes water and solute transfers between mobile and immobile domains. We considered flat bare soils under atmospheric boundary conditions with identical initial pressure head profiles. We targeted instantaneous and mean annual pesticide concentration values at 1-m depth as relevant output variables. Reference values for most of the parameters were obtained from in situ or laboratory measurements. Automation of parameter set generation and input formatting was achieved using SENSAN. We used a one-group-at-a-time sensitivity analysis to isolate and identify the effect of single parameter variations whose ranges were potentially different between topsoil layers (Group 1) and deep layers (Group 2). Sensitivity was analyzed by calculating the time-dependent ratio of variation, i.e., the ratio of relative variation in output concentration to relative variation in parameter input values. As found for other single- or dual- permeability models, transient-MIM HYDRUS-1D was highly sensitive to parameters related to pesticide degradation and sorption, especially the Freundlich exponent associated with nonlinear sorption. Variations in the parameter n of the Mualem–van Genuchten functions had also a very significant impact. Among the MIM parameters, only saturated immobile and mobile water contents were very sensitive parameters, especially those of the topsoil layers. Parameter sensitivities hardly varied among the three soils, but this could be due to their limited contrast.