The use of irrigation systems in rice and other crops cultivated under aerobic conditions in lowland leveling soils has increased worldwide. This study aimed to evaluate the impact of land leveling operations on the soil physical quality (SPQ), mainly on water retention and aeration in a lowland soil in Southern Brazil. A 10 × 10 m-grid was established before and after land leveling in a 1.0 ha-experimental area, where disturbed and undisturbed soil cores were sampled to measure soil texture, organic carbon, bulk density, water retention curve, total porosity, macro, and microporosity at each point location in the 0–0.20 m soil layer. Based on the Spearman correlation results, land leveling negatively affected the majority of the evaluated soil physical properties and SPQ indices. The hydraulic-energy-based indices significantly correlated with other physical properties before and after leveling operations, indicating their capacity to capture the soil structure changes. Likewise, the absolute aeration energy index (Aa-pF) strongly correlated with microporosity emphasizing its application to examine SPQ in land leveling areas. Semivariogram models were fitted to measured data for kriging a spatial variability map for each soil property. Land leveling increased all practical ranges and the goodness-of-fit of the hydraulic-energy indices, decreasing their degree of spatial dependence. The maps of the hydraulic-energy indices were useful to identify regions where key-properties and other SPQ indices presented similar behavior becoming additional tools for farmers to mitigate negative effects of leveling on the SPQ to increase the soil water storage, infiltration, and crop water use efficiency.