The Carpathian Basin is home to a number of astatic soda pans which are especially vulnerable to the climate change due to their high degree of hydrological sensitivity. The photosynthetic plasticity of the three most dominant benthic diatom species (Nitzschia aurariae, N. reskovii, N. supralitorea) in a number of soda pans was measured, along with sulphate and chloride ion content; conductivity and temperature gradients were also recorded. On the basis of the maximal photosynthetic activity (Ps), climate models were employed to observe and predict the effects of climate change on photosynthesis over three time-spans: past (1970–2000), recent past (2005–2015) and projected future (2041–2060). Comparing the periods, it becomes apparent that climate change has a significant effect on photosynthesis and the photosynthetically active period of the Nitzschia species, the dominant primary producers in soda pans, by enhancing their photosynthetic activity and extending their vegetation period by two months. Due to the breadth of their ecological niche, the competitive advantages of the diatom species studied in the course of this research as against others are expected to prevail under the conditions predicted by the climate scenario presented here.