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Increased fluorine pollution represents a serious limitation for the productivity of important crops such as beans. The present study was conducted to detect antagonistic/synergistic ion mobility during seed germination in the presence of F contamination (KF and NaF). NaCl was used as a benchmark. The results showed that germination of Jesca, an African (Tanzania) bean variety, significantly dropped with high F levels (10% KF and 3% NaF). High F levels reduced Jesca growth and decreased root and shoot biomass (by 50% and 95% with KF and NaF, respectively). NaF 200 mg kg
−1
had the most depressive effect on the seedling stage. Elevated F levels negatively affected seedling health, revealing toxicity symptoms such as chlorophyll degradation and low photosynthetic activities that degraded after a threshold level of 80 mg kg
−1
. In addition, an inhibitory effect of F on the mineral status of the seedlings, especially on the Ca content, was observed. An opposite trend of endogenous Ca response to NaCl stress was observed. Indeed, while endogenous Ca content increased with increasing NaCl concentration, it decreased when the F level increased. Therefore, tolerance to F at the germination and seedling stages might be used as a criterion for selecting F-tolerant bean varieties.