The durability of mortar and paste mixtures with respect to chloride ion ingress was investigated for binary blends of Portland Cement Calcined Clay, and ternary systems of Limestone Calcined Clay Cement (LC3). Five clays from various sources with different kaolinite content (17–95%) were studied. The main factor controlling the diffusivity of LC3 systems was found to be the kaolinite content of the clay. Resistance to chloride ingress increased to intermediate levels of kaolinite content and then stabilized. An intermediate kaolinite content of around 50% resulted in two orders of magnitude reduction in diffusivity compared to PC, indicating that the use of high grade (expensive) clays is not necessary to obtain good durability. The chloride binding capacity and distribution of bound chloride between Friedel’s salt and C–A–S–H were quantified for the different systems at fixed water to binder ratio of 0.5. The chloride binding capacity appeared to be a minor factor compared to the porosity refinement in the improved durability of LC3 systems.