The muons, charged particles of cosmic origin, have the particularity of being very penetrative. The attenuation of muon flux in matter highlights the quantity of matter (depth x density) passed through. Based on this principle, the muography is a technique allowing the study of the in-situ density of large targets as geological structures. The Temporal Tomography of rock Density using Muon Measurements (T2DM2) aims at characterizing the spatial and temporal density variations with a first application in the unsaturated aquifer of Fontaine-de-Vaucluse located above the LSBB. This thesis work is focused on the numerical simulation of muon flux at depth and a first campaign of measurements during 16 consecutive months at various depths in LSBB galleries. The performed simulations are in agreement with the expected density variations in an hydrogeological context. The influences of the rock atomic composition and of the scattering processes are discussed as well as strategy to reduce the acquisition duration (and/or detection surfaces and/or solid angles). The measurements performed at LSBB allowed to identify areas of lower density such as the X1 point. The acquired data have been corrected thanks to the determination of the barometric coefficient allowing the temporal analysis of muon flux. The comparison of the recorded flux at different depths (~ 60 m, ~ 200 m and ~ 500 m) with the numerical simulations leads to an estimation of the average density of the rocks located above the LSBB of 1.9 ± 0.1 g.cm-3 testifying their important porosity.