Differences between rootstocks, ‘Cleopatra’ mandarin and ‘Carrizo’ citrange, in soil–plant water relations and the influence of these factors on vigor, crop yield, fruit quality and mineral nutrition were evaluated in field-grown Clemenules mandarin trees irrigated at 100% of potential seasonal evaporation (ET_c) (control treatment), or irrigated at 100% ET_c, except during Phases I and III of fruit growth and post-harvest when no irrigation was applied (deficit irrigation (DI) treatment), for 3 years. Differences between rootstocks in plant–soil water relations were the primary cause of differences among trees in vegetative development and fruit yield. After 3 years of DI treatment, trees on ‘Cleopatra’ showed more efficient soil water extraction than trees on ‘Carrizo’, and maintained a higher plant water status, a higher gas exchange rate during periods of water stress and achieved faster recovery in gas exchange following irrigation after water stress. The DI treatment reduced vegetative development more in trees on ‘Carrizo’ than in trees on ‘Cleopatra’. Cumulative fruit yield decreased more in DI trees on ‘Carrizo’ (40%) than on ‘Cleopatra’ (27%). The yield component most affected by DI in ‘Cleopatra’ was the number of fruit, whereas in ‘Carrizo’ it depended on the severity of water stress reached in each phase (severe water stress in Phase I affected mainly the number of fruit, whereas it affected fruit size the most in Phase III). In the third year of DI treatment, water-use efficiency decreased sharply in trees on ‘Carrizo’ (70%) compared to trees on ‘Cleopatra’ (30%). Thus, trees on ‘Cleopatra’ were able to tolerate moderate water stress, whereas trees on ‘Carrizo’ were more sensitive to changes in soil water content.