Cyanobacteria and microalgae present in the aquatic or terrestrial environment may be emitted into the air and transported along with air masses over long distances. As a result of staying in the atmosphere, these organisms may develop a greater tolerance to stressful factors, but this topic is still relatively unknown. The main aim was to show an autecological characteristic of some airborne microalgae and cyanobacteria strains by a factorial laboratory experiment approach, including changes in irradiance, temperature, and salinity conditions. The additional purpose of this work was also to present part of the Culture Collection of Baltic Algae (CCBA) collection, which consists of airborne algae (AA) isolated from the atmospheric air of the southern Baltic Sea region. Altogether, 61 strains of airborne cyanobacteria and microalgae from the southern Baltic Sea region were isolated from May 2018 to August 2020. Selected microorganisms were tested in controlled laboratory conditions to identify their response to different irradiance (10–190 µmol photons m−2 s−1), temperature (13–23 °C), and salinity conditions (0–36 PSU). The highest numbers of cells (above 30 × 105 cell mL−1) were recorded for cyanobacterium Nostoc sp., and for diatoms Nitzschia sp., Amphora sp., and Halamphora sp. We found that for cyanobacterium Nostoc sp. as well as for green alga Coccomyxa sp. the maximum cell concentrations were recorded at the salinity of 0 PSU. Moreover, cyanobacteria Planktolyngbya contorta, Pseudanabaena catenata, Leptolyngbya foveolarum, Gloeocapsa sp., and Rivularia sp. were able to grow only at a salinity of 0 PSU. On the other hand, in the range of 16–24 PSU, the highest cell numbers of examined diatoms have been identified. Our research provided that deposited airborne microalgae and cyanobacteria showed full colonization potential. The present experiment suggests that the adaptive abilities of microorganisms, in particular those producing toxins, may contribute to the spread in the future. Thus, it may increase human exposure to their negative health effects. Any distinctive adaptations of the genera give them an additional competitive advantage and a greater chance for territorial expansion.