Recent studies have shown that the behaviour and development of coral reef fish larvae is hampered by projected future CO2 levels. However, it is uncertain to what extent this effect also occurs in temperate species. The effects that elevated pCO2 (2000 µatm) levels, which are expected to occur in coastal upwelling regions in the future, have on shoaling behaviour and lateralization (turning preference) of fish, were tested in temperate sand smelt Atherina presbyter larvae. The hypothesis that behavioural changes are caused by interference of high CO2 with GABA-A receptor function was tested by treating larvae with a receptor antagonist (gabazine). Routine swimming speed did not differ between control and high pCO2, but exposure to high pCO2 for 7 days affected group cohesion, which presented a more random distribution when compared to control fish. However, this random distribution was reversed after 21 days of exposure to high CO2 conditions. Lateralization at the individual level decreased in fish exposed to high pCO2 for 7 and 21 days, but gabazine reversed this decline. This adds to the growing body of evidence that the effects of a more acidified environment on fish larvae behaviour are likely due to altered function of GABA-A receptors. Overall, our results suggest that future pCO2 levels likely to occur in temperate coastal ecosystems could have an adverse effect on temperate larval fish behaviour.