Management systems may lead to a loss of soil physical quality as a result of removal of the plant cover and excessive agricultural mechanization. The hypothesis of this study was that the soil aggregate stability, bulk density, macro- and microporosity, and the S index and saturated hydraulic conductivity may be used as indicators of the soil physical quality. The aim was to study the effects of different periods and managements on the physical attributes of a medium-textured Red Oxisol under soybean and corn for two growing seasons, and determine which layers are most susceptible to variations. A completely randomized experimental design was used with split plots (five treatments and four layers), with four replications. The treatments in 2008/09 consisted of: five years of no-tillage (NTS5), seven years of no-tillage (NTS7), nine years of no-tillage (NTS9), conventional tillage (CTS) and an adjacent area of native forest (NF). The treatments were extended for another year, identified in 2009/10 as: NTS6, NTS8, NTS10, CTS and NF. The soil layers 0-0.05, 0.05-0.10, 0.10-0.20 and 0.20-0.30 m were sampled. The highest S index values were observed in the treatment CTS in the 0-0.05 m layer (0.106) and the 0.05-0.10 m layer (0.099) in 2008/09, and in the 0-0.05 m layer (0.066) in 2009/10. This fact may be associated with soil turnover, resulting in high macroporosity in this treatment. In contrast, in the NTS, limiting macroporosity values were observed in some layers (below 0.10 m³ m-3). Highest aggregate stability as well as the highest saturated hydraulic conductivity (Kθ) values were observed in NF in relation to the other treatments. In 2009/10, the Kθ in NF differed only from NTS10. This study showed that the use of the S index alone cannot be recommended as an absolute indicator of the soil physical quality, even at values greater than 0.035.