Bougainvillea is widely used as flowering shrub in gardening and landscaping in the Mediterranean region characterized by limited water supply. The evaluation of deficit irrigation as a possible technique to improve water productivity and selection of genotypes that can better withstand soil water deficits are essential for sustainable production. A greenhouse experiment was conducted to determine the effects of deficit irrigation on three potted Bougainvillea genotypes [B. glabra var. Sanderiana, B. ×buttiana ‘Rosenka’, B. ‘Lindleyana’ (=B. ‘Aurantiaca’)] grown in two shapes, globe and pyramid, on agronomical and physiological parameters. Irrigation treatments were based on the daily water use (100%, 50%, or 25%). The shoot, total dry biomass, leaf number, leaf area, and macronutrient [nitrogen (N), phosphorus (P), and potassium (K)] concentration decreased in response to an increase in water stress with the lowest values recorded in the severe deficit irrigation (SDI) treatment. At 160 days after transplanting (DAT), the percentage of total dry biomass reduction caused by irrigation level was lower in B. ×buttiana ‘Rosenka’ compared with B. glabra var. Sanderiana and B. ‘Lindleyana’ (=B. ‘Aurantiaca’). At 160 DAT, the flower index increased in response to an increase in water stress with the highest values recorded under both moderate deficit irrigation (MDI) and SDI for B. ×buttiana ‘Rosenka’. The biomass water use efficiency (WUE) increased under water stress conditions with the highest values recorded in B. glabra var. Sanderiana and B. ×buttiana ‘Rosenka’ grown under MDI (average 1.43 and 1.25 g·L−1, respectively) and especially with SDI (average 1.68 and 1.36 g·L−1, respectively). A number of tolerance mechanisms such as increase in stomatal resistance, decrease in leaf water potential, and decrease in leaf osmotic potential have been observed, especially under SDI. The MDI treatment can be used successfully in Bougainvillea to reduce water consumption while improving the overall quality and WUE, whereas the genotypes B. glabra var. Sanderiana and B. ×buttiana ‘Rosenka’ could be considered suitable for pot plant production.