Spatial variability of hydro‐physical properties has long been observed, whereas temporal variation is much less documented and considered in studies and applications, particularly of paddy clay soils under different cropping systems. The objective of this study was therefore to assess the seasonal‐ and inter‐seasonal variation of selected hydro‐physical properties of a paddy clay soil under different rice‐based cropping systems with contrasting tillage. In a long‐term experiment, plots were arranged in a randomized complete block design with four treatments and four replications: (i) rice–rice–rice; (ii) rice–maize–rice; (iii) rice–mung bean–rice; and (iv) rice–mung bean–maize. Soil samples were collected at three depths (0–10, 10–20 and 20–30 cm) at three times during two cropping seasons, i.e., 15 days after soil preparation (DASP), 45 DASP and 90 DASP during the winter–spring and spring–summer seasons. Results show that temporal variability of soil bulk density, macro‐porosity (MacP) and matrix‐porosity within both seasons and between seasons was limited for cropping systems with upland crop rotations, whereas within season variation was significant for rice monoculture system. Observed variation in bulk density, matrix‐porosity and MacP was mainly associated with cropping system and soil depth. Field saturated hydraulic conductivity of topsoil showed great temporal variability, both seasonal and inter‐seasonal, in correspondence with MacP (r = 0·58). These results highlight the need of depth differentiated soil sampling and time consideration when evaluating management practices on soil physical properties and modeling the hydrological behavior of paddy soil. Copyright © 2017 John Wiley & Sons, Ltd.