The Czech Republic has diverse soil conditions, which cause notable differences in crop water balance (WB). To assess the long-term crop WB and crop water stress (CWS) intensity in rainfed conditions, four conventional eight- and ten-year crop rotations (CRs) with perennial forage (alfalfa), cereals, oilseeds, root crops and legumes were proposed for a heterogeneous lowland soil region (six texture classes) in eastern Bohemia. Two of the CRs were selected irrespective of the WB (eight-year, C-8; ten-year, C-10), and the other two were designated according to soil water resources and crop water requirements (CWRs) as water-saving (W-S) and water-demanding (W-D) for this region. All CRs had a negative WB on average (i.e., CWRs exceeded the available water resources), with varying degrees of CWS (categories 1 (low) to 4 (high)). The W-S CR reduced the WB deficit relative to the other CRs by omitting maize, sunflower and sugar beet and including sorghum, and expanded the proportion of the area not affected by CWS (categories 1–2) to 33% for predominantly loamy soils. In contrast, categories 1–2 in the C-8, C-10 and W-D CRs represented only 15%, 14% and 7% of the area, respectively. Other areas were significantly affected by CWS (categories 3–4) and showed a high risk of yield reduction. These results may help in implementing sustainable farming systems that consider environmental perspectives related to agricultural water use in Central Europe.