An increase in moisture accelerates the deterioration of a pavement and this is especially so for unbound granular materials below the pavement surface. One of the possible reasons for this accelerated deterioration can be the mineralogical makeup of the aggregates, which can include clays. This research paper discusses the effect of the relative proportions of clay minerals on the performance of different base course materials in repeated load triaxial (RLT) tests considering moisture variation. The materials selected for this study were sourced from greywacke sedimentary rocks from both the North and South Islands of New Zealand. The mineralogical makeup of the clay content present in the base course materials was determined by X-ray powder diffraction (XRD). The performance of these materials was further tested in RLT tests at different moisture and drainage conditions. The results of the XRD and RLT tests showed that aggregates with high relative proportions of smectite clay minerals can decrease the load-bearing capacity of the base course material when moisture is introduced into the pavement materials.