California faces complicated water challenges and increased drought that have put pressure on agricultural systems to cut back on water consumption. Responding to changes in water supply and improving adaptive capacity requires that knowledge and expertise be available to growers and water managers. Water budgets are useful tools that aid in evaluating availability, change, and sustainability of water resources, however water budget components can be difficult to measure due to complex heterogeneity and inherent environmental physical properties. Capturing changes in soil moisture (ΔS) in systems with high clay content soils is notoriously complicated due to interferences from shrink-swell potential and soil-sensor contact. Using winter-cropped, fallowed rice fields in the Sacramento Valley, CA as a case study, we explore water budgets as a tool to inform water management and ecological enhancement while simultaneously evaluating time domain reflectometry (TDR) soil sensors’ ability to measure ΔS in clayey soils. We examined spatial and temporal patterns of water budget components for an irrigated winter crop, an unirrigated winter crop, and a fallow field. During the extremely dry conditions of the 2020-21 water year, the irrigated winter crop and fallow site had a similar seasonal ΔS, while the unirrigated winter crop had much greater soil water depletion. We found the TDR sensor overestimated the magnitude of ΔS during precipitation and irrigation events when compared to recorded precipitation and underestimated ΔS during dry periods when compared to manually collected soil cores, but adequately captured patterns of infiltration and saturation in the soil profile.