Uranium (U) is difficult to be transported from roots to leaves, but it has been reported to inhabit photosynthesis in leaves, so how does this work? In the present study, the effects of U (0–25 μM) on the development and photosynthesis in V. faba seedlings were studied under hydroponics. The results showed that U significantly inhibited the growth and development of V. faba plants, including decreased biomass, water content, lateral root number and root activity. U also led to a large accumulation of reactive oxygen species (ROS) in the leaves which affects leaf structural traits (e.g., decreased leaf area and chlorophyll a content). When U concentration was 25 μM, the net photosynthetic rate (Pn) and transpiration rate (Tr) were inhibited, which were only 66.53% and 41.89% of the control, respectively. Further analysis showed that the stomatal density of leaves increased with the increase of U concentration, while the stomatal aperture and stomatal conductance (Gs) were on the contrary. The results of chlorophyll fluorescence showed that the non-photochemical quenching coefficient (NPQ) increased and the electron transfer rate (ETR) decreased after U exposure, but fortunately, photosystem II (PSII) suffered little damage overall. In conclusion, the accumulation of U in the roots inhibited the root activity, resulting in water shortage in the plants. To prevent water loss, leaves have to regulated stomatal closure at the cost of weakening photosynthesis. These results provide a new insight into the mechanism by which U affects plant photosynthesis.