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Investigating the effects of various agricultural management systems on soil hydraulic properties in long-term field experiments allows farmers to evaluate their efficacy in mitigating the effects of droughts and floods, which are expected to intensify in the coming decades. This study's main objective was to quantify soil structural and hydraulic properties in plots under organic manure, organic leguminous, and conventional agricultural management and related tillage practices at Rodale Institute's Farming Systems Trial. Soil cores were collected at depths of 0–10, 10–20, and 20–30 cm and analyzed for soil water retention, saturated hydraulic conductivity (Ksat), soil organic C (SOC), bulk density, and particle size distribution. Management practices had a measurable effect on SOC and bulk density, but not on Ksat, the parameters of the soil water retention model (rm and σ), or the calculated indicator water content values: field capacity (θfc), wilting point (θwp), plant available water (θpaw), and air capacity (θAirCap). Tillage practices (no-tillage vs. tillage) had a measurable effect on SOC, bulk density and θAirCap, but not on Ksat, θfc, θwp, or θpaw. Significant differences by depth were observed for θfc, θwp, θpaw, θAirCap, SOC, and bulk density, but not for Ksat. Our results suggest that relatively minor differences between management practices may be insufficient for generating quantifiable differences in soil structure, and more substantial changes to management practices will be necessary to achieve the outcomes for developing climate-resilient agricultural soils.