We studied the long-term impact of contrasting tillage and cover cropping systems on soil structure and hydraulic properties. Complete water retention and conductivity curves for the top (0-5 cm) and subsurface (20-25 cm) soils were characterized and contrasted. Dynamic water storage and retention were evaluated using numerical simulations in HYDRUS-2D software. Compared with standard-till (ST) and no-cover-crop (NO) systems, soils under no-till (NT) and cover cropping (CC) systems showed improved soil structure in terms of pore size distribution (PSD). Changes in hydraulic conductivity (K) under these systems led to an increased infiltration rate and water retention. However, NT and CC plots had lower water content at field capacity (33 kPa suction) and lower plant-available water (PAW) compared with ST and NO plots. Numerical simulations, however, showed that NT and CC plots have higher water storage (albeit marginal in magnitude) and water availability following irrigation. Because the numerical simulations considered retention and conductivity functions simultaneously and dynamically through time, they allow the capture of hydraulic states that are arguably more relevant to crops. The study concludes that the long-term practices of NT and CC systems were beneficial in terms of changes to the PSD. NT and CC systems also marginally improved soil water conductivity and storage at the plot scale.