Deep geological repositories are considered as suitable solutions for the disposal of high level nuclear wastes. In several repository concepts (e.g. in Spain and Switzerland), bentonites are selected as the main component of the engineered barrier to be placed between the metallic canister containing the waste and the host rock. The bentonite is emplaced by compaction in unsaturated conditions and will experience wetting and drying processes during the life of the repository. An initial saturation of the barrier is expected upon uptake of water form the host rock. Desaturation will occur as a consequence of the heat emission from the waste. A deep understanding of the water retention behaviour (i.e. the relationship between the suction and degree of saturation) is a fundamental requirement in order to analyse and predict the behaviour of the bentonite based engineered barrier. The retention behaviour is strictly related to the microstructural asset of the material. Bentonites are highly swelling materials and they experience strong modifications of their fabric when subjected to changes in their water content. Interestingly, the link between the evolution of the retention behaviour and the structural modifications during wetting and drying episodes has not been deeply investigated. In this paper we analyse the retention behaviour of a compacted bentonite (granular MX-80) along wetting and drying cycles; also we establish a link between the evolution of the retention behaviour during suction cycling and the structural changes undergone by the material. To this regard, a new protocol has been designed to analyse the retention behaviour of swelling materials. The developed experimental technique involves the control of the water content of the bentonite in constant volume conditions and the measurement of the total suction after equalization. The protocol allows to collect representative samples for microstructural investigations at different stages of the imposed hydraulic stress path. Microstructural analyses were run by combining mercury intrusion porosimetry tests and SEM observations. Results obtained on bentonite samples prepared at different initial densities are presented and discussed. An irreversible modification of the retention behaviour was observed once the material approached the fully saturated state during the first wetting. The water retention capacity of the material was increased as a result of such modification. The microstructural analysis allowed relating this change in the retention properties to a strong modification of the fabric. A clear transition from a double-structured to a single-structured porosity network was registered during the first wetting; this change in the fabric appeared to be permanent in the following suction cycles. Available information on the hydration of smectite particles is used to relate the microstructural evolution with the change in the retention properties. This correlation indicates the evolution of an active porosity at the particle level within the microstructure which consequently affects the macroscopic response of the bentonite in terms of the water retention behaviour.