Long-term water infiltration into porous media, like clastic deposits, causes colmatage (clogging), which is expressed by the decrease of permeability. It is caused by progressive filling of pore spaces with fine particles carried in suspension (mechanical colmatage) and minerals precipitated from water (chemical colmatage or biochemical colmatage, when the process is affected by bacterial activity). Although this material is introduced into the sediment after deposition, it does not destroy the primary framework of it but it only coats grains and fills voids. This process results in some characteristic microstructures that are called 'clogging microstructures'. The research included: (1) experiments on sands exposed to mechanical colmatage in laboratory conditions, which aimed to describe clogging microstructures and to examine the effects of grain size distribution on the rate and degree of clogging; (2) field and laboratory studies of deposits in which colmatage occurred in natural conditions in the infiltrating water intake 'Debina' in Poznan, Poland. The main goal of the research was to identify post-depositional changes that took place in fluvial deposits affected by forced river water infiltration in the Warta River valley. Examples are presented of clogging microstructures formed in deposits affected by colmatage in the laboratory and in natural conditions.