Intercropping or agroforestry systems are among the strategies used to prevent soil erosion or crusting and water loss by evaporation in the bare soil during early growth stage of tree crop plantations. However, the pattern of water use in intercropped, juveline orchard crop plantations is still poorly known. This study aimed to evaluate competition or facilitation for soil water stored by cover crops in rotation and the impact of additional fertilization in a juvenile tung-based intercropping system in southern Brazil during the winter and summer periods of 2012/2013 and 2013/2014 growing seasons. A split plot in randomized complete block design arrangement, with four replications, was used comprising crambe winter cover crop plus poultry manure or nitrogen, potassium and phosphorus (NPK) fertilizer; a mixture of oats and vetch, sunflower, and soybean in rotation; and sole tung as control. Cover crop intercropping significantly increased water content of the surface layer of the juvenile tung soil only at the beginning of the second growing season. The cover crops showed interspecific facilitation for water use by tung during the summer period, but no clear-cut trend for the winter cover crops. The additional organic manure did not enhance profile soil water storage. Any of the summer cover crops (soybean, sunflower, or peanut) could be used for soil and water conservation in juvenile tree crop plantations. Further studies are required during the winter season to establish whether the winter cover crops are competitors or facilitators for stored soil water in agroforestry systems.