Wetlands occupy a small percentage of the Earth's surface but provide essential ecosystem services, such as water regulation, carbon cycling and habitat support. Patagonian “Vegas” are unique wetland ecosystems characterised by their groundwater recharge and hydrological dynamics, distinct from the surrounding steppe. These ecosystems play a critical role in supporting livestock with up to six times the forage productivity of the surrounding steppe and in storing over 69 g kg−1 of organic carbon. However, the influence of soil structure parameters (e.g., pore size distribution, bulk density) and soil shrinkage behaviour on soil moisture variability and ecosystem functions in Patagonian wetlands remains poorly understood. This study aimed to assess the physical capacity and intensity parameters of soils, including shrinkage properties, within a micro-watershed in southern Patagonia. Our findings reveal significant spatial variability in soil properties, with bulk density (BD) ranging from 0.12 to 1.81 Mg m−3 across topographic positions. Mineral soils on summits and footslopes exhibited high macroporosity (up to 18.1% of total pore volume at 5 cm depth), which facilitates water movement, while organic soils in the Vega centre had a higher total porosity (up to 88.8%) that enhances water and air retention. The coefficient of linear extensibility (COLE) for organic soils reached a level of 0.078, indicating a high shrinkage capacity. This shrinkage influenced the functionality of the porous system, shifting pore roles between air conduction and water storage as larger pores contracted. These dynamics, driven by climate change and increased drying cycles, may lead to significant shifts in soil functionality and ecosystem resilience. Enhanced understanding of soil physical states and their response to environmental changes can support sustainable management strategies, benefiting local agriculture and preserving these critical ecosystems.