Climate changes alter the environmental conditions which pavement design is based on, invalidating empirical design methods. Transition to mechanistic design requires the ability to model the behaviour of pavement materials under relevant environmental conditions. An accelerated pavement test (APT) is designed to test two instrumented pavement structures under moisture conditions which are altered by raising the groundwater table (GWT). Open-graded and well-graded subbase materials are used to investigate the effect of gradation on moisture dependency. Pavement response behaviour is modelled using a non-linear elastic (NLE) approach. Accumulation of permanent deformation under different moisture conditions is calculated by two models and compared to measured surface rutting. Moisture transport through the structures differs due to the subbase gradation. Increased GWT accelerates the accumulation of permanent deformations in both structures, identified by both models. One model provides a significantly better fit to the subgrade deformations and the width of the rutting profile.