Agricultural management practices can influence soil structure and health in the long term. Hydraulic conductivity (cm/s), indicating the soil's ability to transport water through its profile in both near-saturated (K) and field-saturated conditions (Kfs), is a key parameter to assess soil's hydrological characteristics. This study investigated the impact of two different management practices (soil health versus conventional) on hydraulic conductivity. Two pairs of sites in Olmsted and Freeborn counties of Minnesota, USA, were studied for two years (2022 and 2023) to analyze the variability over the growing season. Results demonstrated that K showed variable response to the agricultural management systems. The values were observed to be higher in conventional fields in June while in August, soil health sites exhibited higher conductivity. The effect of time on K was much stronger (p << 0.01) than management (p > 0.05), while their interaction also significantly influenced the K values (p < 0.01). Field-saturated hydraulic conductivity (Kfs) was found to be higher in conventional fields (p < 0.01) but was also moderately affected by the time of measurement (p < 0.05). It is important to note that K represents hydraulic conductivity of the soil matrix while Kfs accounts for the water flow through soil's structured media (including cracks, wormholes, etc.). Our results suggested that preferential flow paths were more prevalent in conventional fields, while the soil matrix responded differently over the growing season in soil health and conventional fields. Considering the growing focus on soil health practices, this study highlights crucial findings related to the hydrological impacts of different agricultural management systems.