Soil hydraulic properties are needed for modelling of water and substance movement in unsaturated soils. Their direct measurements are difficult, time-consuming and expensive. Therefore, these properties need to be estimated using indirect methods. The objective of this study was to evaluate the effect of micro-aggregates on the estimation of soil water retention. In this study, 74 disturbed and undisturbed soil samples were taken from Guilan province, northern Iran. Bulk density, water content at matric suctions of 5, 25, 33, 100 and 1500 kPa and micro-aggregate size distribution (MASD) were measured. Fractal parameters of the MASD were calculated and used to estimate water content. Estimation of water contents at different matric suctions, were improved significantly, by adding fractal parameters of the MASD to the pedotransfer functions. The most improvement was occurred for θ1500 prediction with the relative improvement of 12.5 and 45.2% for training and testing, respectively. It can be due to the influence of soil micro structure on the water retention at high matric suctions. Smectite clay due to high specific surface area affects soil structure and micro-aggregates and consequently affect water retention. Using the MASD would be useful in the estimation of soil water content in smectitic soils.