Abstract Numerous boreal lakes across the Northern Hemisphere recovering from acidification are experiencing a simultaneous increase in chloride (Cl) concentrations from road salting. Increasing Cl may have profound effects on the lake ecosystem. We examine if an increase in Cl from road salting has modified the recovery of the microcrustacean community in an acidified boreal lake undergoing chemical recovery (study lake). Results from the study lake were compared with an acidified “reference lake”. The community changed during the study period in the study lake mainly driven by the reduction in acidification pressure. Despite the community changes and an increase in species richness, the absence of several acid sensitive species, previously occurring in the lake, indicates a delayed biological recovery relative to the chemical recovery. Moreover, changes in occurrence of acid sensitive and acid tolerant species indicated that the biological recovery was slower in the study lake compared to the “reference”. Although recurrent episodes of high aluminum and low pH and decreasing Ca are likely important factors for the delay, these do not explain, for instance, the shift from Cyclops scutifer to Bosmina longispina in the study lake. Although the contribution of Cl was not significant, the correlation between Cl and the variation in microcrustacean community was twice as high in the study lake compared to the “reference”. We argue that small, sheltered forest lakes may be especially sensitive to increased Cl levels, through changes in pattern of stratification, thus providing a mechanism for the shift from C. scutifer to B. longispina. The reduction of the acidification pressure seems to override the Cl effects on microcrustaceans at low Cl levels in salt-affected lakes recovering from acidification. However, prognoses for growing traffic and increasing road salting raise concern for many recovering lakes located in proximity to roads and urbanized areas.