A better understanding of spatial soil variability, its development over time (pedogenesis) and its functional relationships to recent processes in soil landscapes is one of the biggest challenge in soil science. This paper presents three case studies on the influence of soil pattern - developed in geological time scales - on actual matter transport: (i) solid phase transport in agricultural landscapes, (ii) solute transport from forested catchments, and (iii) gas fluxes from agricultural landscapes. In case study I the exclusion of sedimentation zones as well as a segmentation of soil landscapes by digital terrain analysis leads to a more realistic picture of measured erosion rates compared to area-wide modeling. Soil landscape analysis in forested catchments (case study II) results in riparian soils to be most sensitive areas for DOC- and Fe-fluxes between terrestrial and fluvial biogeosystems. Regardless of the absolute or relative acreages the formation of riparian soils as pedochemical barriers or zones of high element mobility determine catchment outputs. In case study III the influence of soil pattern development on the emergence of biogeochemical hot spots in grassland systems is demonstrated. Past solid phase transport (soil erosion) into wet parts of agricultural landscapes led to small fringes of very high CH4 fluxes. The latter are comparable to paddy soils in respect to unit area emissions. They are of relevance for regional methane inventories at least. From the results a generalized concept for soil landscape research is developed. In the so-called "multiscale soil landscape analysis" special emphazis is given to the role of “sensitive areas” in soil landscapes for matter fluxes.