So far, research on inter- and intraspecific teleost brain plasticity across different freshwater environments has been widely conducted. However, insights of brain morphological variation on social and predator avoidance behaviours are lacking. Here, we investigated variation in shape and size of the brain and its six major regions of European minnows (Phoxinus phoxinus) inhabiting Lake Ånnsjön and its tributaries, using geometric morphometrics methods. We also experimentally compared stream and lake fish activity and social behaviour under different feeding and predation regimes. Contrary to our predictions of lake minnows having evolved smaller brains because of living in habitats with reduced environmental complexity compared to their conspecifics in the streams, we found that overall brain size generally did not differ between locations. Instead, brain morphology differed between minnows caught in the lake and streams, with stream minnows showing larger dorsal medulla, telencephalon and olfactory bulbs, and lake minnows presenting larger optic tecta and hypothalamus. Experimental results showed that lake minnows were more likely to engage in social behaviour than those from streams. Our results indicate that while overall allocation of energy to the brain does not change, habitat-specific differences in activity and trophic divergence might predict specialization for different senses, allocating more resources towards different brain regions. In addition, we show how various ecological factors, such as environmental complexity and social organization seem to be reflected in brain shape.