Climate change is transforming marine ecosystems, with rising temperatures and changing salinity patterns expected to reshape plankton communities in the Baltic Sea. As key components of marine food webs and biogeochemical cycles, plankton are highly sensitive to environmental change. Here, we examined the effects of warming and salinity change on plankton communities using a mesocosm experiment at the Tvärminne Zoological Station, Finland. We employed both traditional microscopy-based identification and DNA metabarcoding (18S rRNA and COI markers) to assess shifts in phytoplankton, ciliates, and mesozooplankton. Our findings indicate that salinity primarily affected higher trophic levels, while warming influenced lower ones. Warmer conditions increased community evenness and favoured mixotrophic and heterotrophic taxa, whereas salinity effects were most pronounced in rotifers and copepods, reflecting species-specific tolerances. Interactive effects varied, with salinity sometimes buffering warming impacts and other times intensifying them, highlighting complex stressor interactions. Microscopy allowed for a more precise quantification of plankton abundance, whereas metabarcoding captured a broader taxonomic diversity. Our results suggest that freshening and warming in the Baltic Sea may lead to a shift towards smaller, mixotrophic and bloom-forming plankton species, with potential consequences for ecosystem functioning. This study highlights metabarcoding's value in mesocosm research while emphasising the need to refine molecular techniques for ecological interpretations.