Soil water status, which refers to the wetness or dryness of soils, is crucial for the productivity of agroecosystems, as it determines nutrient cycling and uptake physically via transport, biologically via the moisture-dependent activity of soil flora, fauna, and plants, and chemically via specific hydrolyses and redox reactions. Here, we focus on the dynamics of nitrogen (N), phosphorus (P), and sulfur (S) and review how soil water is coupled to the cycling of these elements and related stoichiometric controls across different scales within agroecosystems. These scales span processes at the molecular level, where nutrients and water are consumed, to processes in the soil pore system, within a soil profile and across the landscape. We highlight that with increasing mobility of the nutrients in water, water-based nutrient flux may alleviate or even exacerbate imbalances in nutrient supply within soils, for example, by transport of mobile nutrients towards previously depleted microsites (alleviating imbalances), or by selective loss of mobile nutrients from microsites (increasing imbalances). These imbalances can be modulated by biological activity, especially by fungal hyphae and roots, which contribute to nutrient redistribution within soils, and which are themselves dependent on specific, optimal water availability. At larger scales, such small-scale effects converge with nutrient inputs from atmospheric (wet deposition) or nonlocal sources and with nutrient losses from the soil system towards aquifers. Hence, water acts as a major control in nutrient cycling across scales in agroecosystems and may either exacerbate or remove spatial disparities in the availability of the individual nutrients (N, P, S) required for biological activity.