Nitrate salts have become of greater importance in the decay of materials from historical buildings due to changes in the environment. This work presents an analytical diagnosis methodology to evaluate the impact of nitrate salts in mortars and bricks, combining noninvasive and microdestructive analytical techniques together with chemometric and thermodynamic data analyses. The impact of nitrate salts cannot be well ascertained if other soluble salts are not taken into account. Therefore, the principal results from this work relate to nitrate salts but some results for other kinds of salts are included. Data from Raman microprobe spectroscopy and micro X-ray fluorescence (micro-XRF) are used to characterise the original composition and a first approximation of the nature of the decay compounds, mainly nitrates. The soluble salts are extracted and the anions and cations are quantified by means of ion chromatography with conductimetric detection for anions/cations and inductively coupled plasma mass spectrometry (ICP/MS) for cations. The values obtained allow two different data treatments to be applied. First, chemometric analysis is carried out to search for correlations among anions and cations. Second, thermodynamic modelling with the RUNSALT program is performed to search for environmental conditions of soluble salt formation. All the results are finally used to diagnose the impact of nitrates.