The excavation of a tunnel through a mudstone formation provides an opportunity to examine the effects of the modification of the physical and chemical environment on the rock. The mineralogical and chemical consequences of hydration-dehydration cycles and of oxidation have been evaluated in the case of the Toarcian mudstone formation at the Tournemire experimental site (France). Studies by X-ray diffraction and tansmission electron microscopy of both altered and preserved samples show that the introduction of air and condensed water causes the oxidation of pyrite and the subsequent generation of acid and sulphate-rich waters at the micron scale, in the local environment of pyrites. The fluid-clay particle interactions around the oxidized pyrites induce: (1) a statistical enrichment in Si of the I-S clay minerals; (2) an increase in the Fe(III)/Fe total ratio in some of the I-S particles; and (3) the dissolution of illite layers in mixed-layer I-S. These evolutions are consistent with the results of numerical modelling which reproduced the interaction between the clay particles and the acid water.