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Most methods for mapping groundwater vulnerability are based on the excessively simplistic approach that aquifer recharge is produced by vertical infiltration. The novel Land Use–Intrinsic Vulnerability (LU–IV) procedure assesses groundwater vulnerability to nitrate pollution over the entire territory, including aquifers catchment areas. In this research, it was analysed if the delineation of nitrate vulnerable zones (NVZs) would be improved by introducing a new parameter representing the risk associated with soil permeability (parameter S) in the procedure. Different versions of parameter S were tested: S_HC (risk associated with soil hydraulic conductivity), S_St+G+S (risk associated with the stone, gravel and sand fraction of the soil) and S_C (risk associated with the clay fraction). The study was undertaken in the catchment areas of the Oja and Tirón alluvial aquifers (Spain). The efficacy of the following six models was compared: Model 1 (original LU–IV procedure), Model 2 (LU–IV’ procedure using parameter S_HC), Model 3 (LU–IV’ procedure using parameter S_St+G+S), Model 4 (LU–IV’ procedure using parameter S_C), Model 5 (LU–DRASTIC–COP procedure, based on DRASTIC–COP method), and Model 6 (designated NVZ). Catchment scale validations of the six models showed similar, highly significant correlations between the percent coverages of the estimated NVZs and those of the alluvial areas polluted by nitrate for Models 1 to 4. Models 5 and 6 did not show any significant results. In light of these results, Models 1 to 4 were considered the best predictors of nitrate pollution and the best methods for NVZ delineation. Results support the idea that including a parameter S in the LU–IV’ procedure is not essential since equivalent results were obtained from the original LU–IV procedure. So, the LU–IV procedure should be considered the best and simplest method of those tested for accurately delineating NVZ.