Abstract Freshwater salinization is an increasing threat to lakes worldwide, but despite being a widespread issue, little is known about its impact on biological communities at the base of the food chain. Here we used a mesocosm set‐up coupled with modern high‐frequency sensor technology to identify short‐ and longer‐term responses of phytoplankton to salinization in an oligotrophic lake. We tested the effects of salinization over a gradient of increasing salt concentrations that can be found in natural lakes exposed to road salt contamination (added salt range: from 0 to 1500 mg Cl− L−1). The high‐frequency chlorophyll‐a (chl‐a) fluorescence measurements showed an increasing divergence of chl‐a concentrations along the salinization gradient over time, with substantially lower concentrations at higher salt levels. At the sub‐daily scale, we found a profound suppression of day–night signal cycles with increasing salinity, which could be related to physiological stress due to the impairment of photosynthesis via effects on the photosystem II or potential changes in the active migration of phytoplankton. Community analyses revealed a similar decline pattern for the total phytoplankton biomass and a collapse of the total zooplankton biomass. Interestingly, we found a loss of phytoplankton diversity coupled with a compositional re‐organization involving the loss of dominant green algae but increased biomass of salt‐tolerant cyanobacteria. Altogether, these results suggest that specific cyanobacterial taxa can benefit from freshwater salinization following the collapse of dominant phytoplankton competitors and zooplankton herbivores. The results also highlight the value of autonomous sensor technology to capture novel, small‐scale ecological responses to freshwater salinization, and thereby to track fast changes in primary producer communities.