The detection of R6G on nanoporous susbtrates at low concentrations (10(-4) M < C < 10(-7)M) was studied coupling its thermodynamic adsorption properties and its Raman response. Two susbtrates were used, they consist in a mesoporous silica matrix in which Ag or Au nanoparticles are incorporated. From a thermodynamic point of view, it was evidenced, using adsorption isotherms and enthalpies, that R6G presents a higher affinity towards Ag@SiO2 than Au@SiO2. Furthermore, for C > 1.10(-6) M, it was evidenced that R6G Raman response does not depend on metal chemical nature. It is linearly correlated to R6G adsorbed amounts, evidencing the pre-concentration property of the substrates. For lower concentrations, differences were observed in Raman responses. For C = 1.10(-6) M, the Raman bands of R6G adsorbed on SiO2 and Au@SiO2 are similar to those found at higher concentrations. For Ag@SiO2, two new bands, corresponding to bending modes of ethylamine groups, are present as well as the band related to Ag-N stretching mode. This was explained by the specific interaction developed between R6G and Ag@SiO2. For C = 1.10(-7) M, only the two bands related to R6G ethylamine groups are present for all substrates and a Raman signal enhancement was found for Ag-based substrate.