Perennial biofuel and cover crops systems are important for enhancing soil health and can provide numerous soil, agricultural, and environmental benefits. The study objective was to investigate the effects of cover crops and biofuel crops on soil hydraulic properties relative to traditional management for claypan soils. The study site included selected management practices: cover crop (CC) and no cover crop (NC) with corn/soybean rotation, switchgrass (SW), and miscanthus (MI). The CC mixture consisted of cereal rye, hairy vetch, and Austrian winter pea. The research site was located at Bradford Research Center in Missouri, USA, and was implemented on a Mexico silt loam. Intact soil cores (76‐mm diam. by 76‐mm long) were taken from the 0–10, 10–20, 20–30, and 30–40 cm depths with three plot replicates and two sub‐samples per plot replicate per depth. Soil hydraulic properties evaluated for each sample included: saturated hydraulic conductivity (Ksat), water retention, bulk density, and pore size distributions. Results showed with the test of Duncan's least significant differences that treatments of MI (1.18 Mg m⁻³) and SW (1.21 Mg m⁻³) had lower values of bulk density averaging across soil depth than CC (1.27 Mg m⁻³) and NC (1.31 Mg m). Management systems significantly increased Ksat with the biofuel treatments at 0–10 cm compared to NC system. The MI management showed a significant increase in macroporosity and fine mesoporosity as compared to other management systems. Slight changes have occurred in the measured soil physical properties for CC system compared to NC plots. Overall, increasing soil organic matter from more plant roots from long‐term biofuel cropping systems can improve soil water storage and crop productivity.