This study examines physiological and biochemical changes in three Moroccan varieties of young olive trees (Olea europaea L.) grown under three different water regimes (control, moderate stress and severe stress). Leaf relative water content (RWC), water potential (Ψw), transpiration rate (E), stomatal conductance (gs), maximum quantum efficiency of PSII (Fv/Fm), the contents of total chlorophyll (TCC), proline (ProC) and soluble sugars (SSC) were measured at the flowering stage during three growing seasons (2015, 2016 and 2017). ANOVA analyses showed that the effect of the water regime was predominant in all of the examined parameters, except for Fv/Fm, which was under the effect of both water regime and growing season. Impacts of variety and interactions were of lesser magnitude. Water deficit reduced E, Ψw and gs by 25%, while its effect on RWC and Fv/Fm was a decrease of about 7%; however, increases in SSC and ProC were more than 10%. Among the growing seasons, 2015 flowering displayed the lowest values for RWC, Ψw, E, gs, TCC and Fv/Fm, and the highest for ProC and SSC. Among plant varieties, no significant differences were observed. The three principal component (PC) axes accounted for 91% of total variance. PC1 was better explained by the water regime, while the growing season fitted PC3 variability. Correlation studies highlighted significant associations between most parameters. Positive relationships were found between RWC, Ψw, E, gs, Fv/Fm and TCC, while all of these parameters were negatively linked to ProC and SSC.