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<i>Arabidopsis thaliana</i> SYNAPTOTAGMIN 1 (AtSYT1) was shown to be involved in responses to different environmental and biotic stresses. We investigated gas exchange and chlorophyll <i>a</i> fluorescence in Arabidopsis wild-type (WT, ecotype Col-0) and <i>atsyt1</i> mutant plants irrigated for 48 h with 150 mM NaCl. We found that salt stress significantly decreases net photosynthetic assimilation, effective photochemical quantum yield of photosystem II (Φ_PSII), stomatal conductance and transpiration rate in both genotypes. Salt stress has a more severe impact on <i>atsyt1</i> plants with increasing effect at higher illumination. Dark respiration, photochemical quenching (qP), non-photochemical quenching and Φ_PSII measured at 750 µmol m⁻² s⁻¹ photosynthetic photon flux density were significantly affected by salt in both genotypes. However, differences between mutant and WT plants were recorded only for qP and Φ_PSII. Decreased photosynthetic efficiency in <i>atsyt1</i> under salt stress was accompanied by reduced chlorophyll and carotenoid and increased flavonol content in <i>atsyt1</i> leaves. No differences in the abundance of key proteins participating in photosynthesis (except PsaC and PsbQ) and chlorophyll biosynthesis were found regardless of genotype or salt treatment. Microscopic analysis showed that irrigating plants with salt caused a partial closure of the stomata, and this effect was more pronounced in the mutant than in WT plants. The localization pattern of AtSYT1 was also altered by salt stress.