AbstractCharacterization of spatial and temporal variability in water flow and solute transport to foster better land management in salt‐affected landscapes requires direct hydrological observation, for example using suites of nested piezometers and dip wells. Such methods are costly to install and produce data with low spatial density, so are not ideal for supporting within‐field scale land management decisions. We present a new methodology to characterize water‐flow systems in salt‐affected landscapes using trends in shallow (<1 m) down‐profile soil salinity based on electrical conductivity of saturated paste extract (ECse) and salts (that is the water extractable major ions of Ca, K, Mg, Na, P, Cl and S mg/kg) from a range of topographic settings. This involved coupling seasonal (late winter and late summer) salinity trends with clay percent (for soil morphology) and terrain patterns to understand the connectivity between perched and deep groundwater systems in a 120 ha catchment in the Mount Lofty Ranges, South Australia. From investigations at 19 sites in the catchment comprising toposequences or paired sites (in close proximity, but in different topographic settings), soil salinity trends revealed four hydro‐pedological systems: (i) a perched freshwater system with no hydraulic connectivity to the deep groundwater in upper slopes, (ii) an intermediate system comprising perched freshwater connected to a deep groundwater system in mid and upper slopes, (iii) a deep groundwater system in upper slopes, and (iv) a deep groundwater system in lower slopes. Although most of the 19 sites proved non‐saline, seasonal changes in ECse and ion concentration along with topography and soil morphology were sufficient to characterize the hydro‐pedological systems. We assigned these systems to a newly developed salinity classification based on dominant soil‐regolith‐hydrological processes and designed to support land management decisions. Conceptual hydro‐pedological models for each system were constructed to illustrate and explain the important interactions in each and how these relate to the new salinity classification. We propose that the methodology based on seasonal monitoring offers a new approach to landscape‐based hydro‐pedological characterization without reliance on the traditional groundwater monitoring methods. The new method offers wider access to catchment hydro‐pedological information to support better land management decisions in sloping landscapes subject to salinity.