It is well-known that supplementary cementitious materials (SCMs) and low water-to-binder (w/b) ratio increase autogenous shrinkage, but the impact on microcracking and long-term transport properties is less understood. This paper examines the effect of microcracking induced by autogenous shrinkage on transport properties of concretes cured up to ~3.6 years. Variables include SCM type (9% SF, 70% GGBS), w/b ratio (0.20–0.45), maximum-aggregate-size (MSA: 5–20 mm) and shrinkage reducing admixture (SRA). Oxygen diffusivity, permeability and water sorptivity were correlated with microcracks characterised using laser scanning confocal microscopy and 3D X-ray microtomography. Results show greater microcracking in mixes containing SCMs, low w/b ratio and large MSA. At the same w/b ratio and binder type, strong positive correlations are observed between transport and microcracking with increasing MSA, confirming the negative impact of autogenous shrinkage. SRA was effective in reducing these effects. The significance is compared with drying shrinkage and implications for durability are discussed.