Nitrogen pollution and excessive salinity are commonly regarded as one of the major environmental concerns in recent decades in many urban environments. Although in urban areas lichens are exposed to both salt and nitrogen stress, no studies have been conducted to date on the simultaneous impact and interaction of these factors on lichen physiology. The aim was to determine the effect of various combinations of NaCl and NH4NO3 doses on the physiology of epigeic lichen Cladonia rei. We also aimed to compare the response of lichens collected from polluted and unpolluted sites to verify whether lichens exposed to different levels of environmental stress in their native environment will react differently. The combined salt-nitrogen treatment caused significant disturbances in the integrity of cell membranes and chlorophyll fluorescence parameters. The most detrimental effect concerned the loss of cell membrane integrity, which suggests that this parameter can serve as a relevant indicator of acute salt-nitrogen stress incidents. Salt stress decreased the photosynthetic efficiency 1 h after exposure, but after 72 h, the FV/FM returned to the level characteristic of healthy lichens in experimental groups without and with small doses of ammonium nitrate. In contrast, recovery was not possible in combination with high nitrogen doses. This indicates that exposure to short-term salt stress in a nitrogen-poor environment only causes a temporary reduction in photosynthetic efficiency, but in urban eutrophic environments may have more serious consequences. The weakened physiological condition of the mycobiont manifested by an increased level of cell membrane damage and a persistent decrease in the photosynthetic efficiency of the photobiont in lichens growing along the roads may indicate an excess of nitrogen in the environment, enhanced by the effect of salt. Lichens collected from a heavy-metal-polluted habitat responded more strongly than those from an unpolluted habitat suggesting that in lichens previously affected by certain harmful factors, exposure to another stress factor may lead to greater disturbances. This is of particular importance for lichens inhabiting the vicinity of roads, since they are also under the influence of other pollutants emitted by road traffic.