Cover crops have multiple benefits, such as improving water quality, providing a green manure effect, and storing carbon in the soil. They can, however, reduce drainage significantly during key periods of hydrosystem recharge, especially in winter. The objective of this study was to evaluate the influence of cover crops and/or crop diversification at the watershed scale on water in the downstream watershed of the Aveyron River, based on three scenarios with different management practices. It is an illustrative case study of situations of water imbalance involving 1150 farms, with agricultural fields covering 40,000 ha, of which ca. 40% may be irrigated. The MAELIA model was used to simulate 10 years (2007-2016) of dynamics to estimate the influence of cover crops on water flows. Simulations showed that short-duration cover crops terminated in autumn generally had little influence on water: they decreased drainage slightly in autumn, but the recharge in winter compensated for this decrease and thus did not influence the water dynamics or yields of the succeeding cash crops. Although long-duration cover crops grow for a longer period and are sown more frequently in fields, they also had relatively little influence on water in the region, except for decreasing drainage. A scenario with long-duration cover crops and diversification of rotations was a good compromise for quantitative water management. Diversifying rotations, notably by replacing maize with crops that required less water, compensated for potential negative effects of long-duration cover crops. Although this scenario increased variability depending on the weather year and reduced autumn drainage, it influenced irrigation withdrawals and river flows little over the 10-year period. However, greater variability occurred at the field scale, where cover crops can have more influence. Thus, it is important to adapt the management practices for cover crops in rotations to decrease negative effects, particularly on water availability, which could increase withdrawals in an area that already has a water deficit, and not to decrease yields and thus farmers' profits. Our results are valid for the study area, but these scenarios should be extrapolated to other soil and climate conditions and other rotations and management systems.