Exploratory data analysis is commonly used in geoscientific research to identify various data populations within datasets. Frequently, the distribution-wise metrics for the statistical centre and spread are combined to define normal (background) ranges of topsoil contents of potentially toxic elements. When decreasing the geographical scale, the survey areas turn too heterogeneous for the statistical definition of a single background range. The traditional solution is the domain approach wherein various data populations (and their statistical parameters) can be attributed to contextual (geological, ecological) information. Nevertheless, summarising the entire data set from large areas as a single statistical entity would provide too much data reduction which would decrease sensitivity of detecting localised anthropogenic contamination and work wrong in areas of geogenic anomalies spatially larger than contamination. In this paper, we tested a novel numerical solution for deriving local distribution-wise baseline values via spatially limited sliding window combined with geographical weighting. Considering environmental variables (soil and topographical properties) at every analysed soil sample point, we extended the geographical kernel weighting approach which considers only spatial dimension (given by geographical coordinates). The advanced version combines two similarity modes to assign highest weights to the nearest points expected to share similar environmental contexts within the user-defined moving kernel. The method was implemented for data-mining in the Czech high-density monitoring data for agricultural soils which had to be firstly regressed to achieve analytical harmony between two distinct extraction methods employed in that monitoring, in particular cold diluted nitric acid and hot aqua regia. After the reliable harmonisation, local baseline values were delivered as the localised outer limits of variation using the proposed double-weighted kernel approach. We compared the estimated localised background ranges for 10 potentially toxic elements (As, Be, Cd, Co, Cr, Cu, Ni, Pb, V, and Zn) with those based on the conventional substrate-wise domain approach and single nationwide legislation thresholds. The comparison was also efficient in identifying an inappropriate aggregation of some geological units. Finally, the kernel approach delivered regional outer limits of variability sensitive to subtle regional variations of topsoil geochemistry.