Lake charr (Salvelinus namaycush) embryos in the later stages of yolk absorption avoided water with pH < 6.0. The addition of inorganic Al (≤ 200 μg∙L−1) did not increase the avoidance response to low pH. Embryos tested just after hatch had little swimming ability and showed no avoidance to acutely lethal H+ (pH 4.0). In vertical substrate-filled tanks that simulated conditions at natural spawning sites, there were no significant effects on embryo survival, or movement within the substrate from pulse exposure (8 h) to low pH (4.5) and elevated Al (100, 200, 500 μg∙L−1). Preference for contact with the substrate appeared to override the avoidance reactions observed in horizontal counter-current tanks. Thigmotaxis, combined with poor swimming ability of embryos, appears to eliminate the possibility that lake charr embryos will effectively avoid the acidic runoff water that enters the rubble of spawning sites during snowmelt.