Spatial variation in the landscape factors climate, geomorphology, and lithology cause significant differences in water quality issues related to land use. The Physiographic Environment Classification (PEC) distinguishes these differences by classifying the landscape's susceptibility to contaminant loss according to the factors that control the hydrochemical maturation of water. PEC accounts for the landscape's ability to generate, retain, attenuate, and transport multiple contaminants, including particulate and dissolved substances. A case study application of the PEC method to New Zealand utilized topographic data and geological survey to classify the country into six classes at Level l (Climate), 36 classes at Level 1–2 (Climate + Geomorphology), and 320 classes at Level 1–3 (Climate + Geomorphology + Lithology). Variance partitioning analysis, applied to New Zealand's national surface water monitoring network (n = 810 stations), evaluated the unique contributions of PEC classes and land use to six water quality variables. Relative to land use, PEC explained 0.6 times (x) the variation in NNN, 1.0x (i.e., the exact quantum of variability as land use) TKN, 1.8x DRP, 2.3x PP, 2.6x E. coli, and 4.3x TURB. Across the six water quality variables, PEC explained 2.1x more variation in riverine contaminant concentrations than land use. After controlling for land use, water quality variables varied significantly between PEC categories and classes (p < 0.05), with the pattern of differences consistent with the conceptual model underlying the classification. Because PEC elucidates the underlying causes of contaminant loss susceptibility, it can be used to inform targeted land management across multiple scales.