Two nanocrystalline palladium-supported tin oxide catalysts for water denitration were synthesized by a modified sol–gel technique using appropriate chloride precursors for both support and active phases, and citric acid to tune the rate of hydrolysis and condensation. The difference among sample preparation procedures refers to the moment of the noble metal loading to the support, as well as to the calcination temperature altitude followed. Thus, mesoporous tin oxide was synthesized by a sol–gel method following calcination at 700°C. The palladium active phase was introduced afterwards by means of palladium chloride solution impregnation, followed by calcination at 400°C (sample 1). Alternatively, simultaneous complexation of both metal and support precursors followed by single calcination at 700°C was applied for preparation of sample 2. The former sample showed higher activity and selectivity in hydro-denitration of water model system initially containing 100 ppm of nitrates. This was explained by preferential textural, morphological and structural properties accomplished by early contact of metal and support nanoparticles, while achieved by calcination at high single temperature forcing diffusion of palladium ions into the tin oxide matrix. The outcome is very well distribution of palladium and strong metal–support interaction leading to multivalent tin. This indicates partly reduced tin oxide formation in the course of its reduction in hydrogen, which may act as active site in denitration reaction.