Rising dissolution of anthropogenic CO2 in seawater may directly/indirectly cause ocean acidification and desalination. However, little is known about coastal physiological functions sensitivity to these processes. Here we show some links between ocean acidification/desalination and physiological functions in Thalassiosira weissflogii. Cell density (CD), protein, chlorophyll a (Chl a), malonaldehyde (MDA), superoxide dismutase (SOD), and carbonic anhydrase (CAs) were determined for the assessment of algal biomass, nutritional value, photosynthesis and respiration, lipid peroxidation, antioxidant capacity, and carbon sequestration ability. The influence of pH on the algal Chl a and MDA were extremely significant (P < 0.01). Salinity (S) on cell density and acidity (pH) on protein was significant (0.01 < P < 0.05). Additionally, a significant negative-correlation was observed between cell density and CAs. CAs and SOD had negatively correlations with CD, Chl a, protein, and MDA under pH or S influence, but positive correlation between themselves. Coastal physiological functions were affected by increasing order was acidification < acidification + desalination < desalination for Chl a and protein, desalination < acidification + desalination < acidification for SOD and CAs. Thus, the ongoing excessive CO2-driven ocean acidification and desalination should be of high attention when assessing the risks of climate change on coastal phytoplankton.