Elevated CO2 in aquatic environments causes weak acidification. When exposed to weak acidification, regardless of life stage, most fishes undergo some degree of hypercapnia (elevation of CO2 in the bloodstream). Hypercapnia negatively affects physiological processes and embryo and larval fish are particularly vulnerable to rises in CO2. The aim of our study was to understand if weak acidification induced by elevated CO2 alters the physiology and behaviour of freshwater Japanese medaka (Oryzias latipes) embryos and larvae. To test this, we treated Japanese medaka embryos and larvae for 24 h with varying levels of weak acidification (pH 7.1 [∼482 μatm], 6.4 [∼2,122 μatm], 6.1 [∼3,280 μatm], 5.8 [∼5,306 μatm], and 5.7 [∼10,130 μatm]) at two developmental stages (72 hpf and 9 dpf). Following the treatment, heart rate, burst activity (movement within the egg), and survival of embryos were quantified. Swimming activity of hatched larvae was also measured. We observed a statistically significant 2-fold decline in heart rate of embryonic Japanese medaka as pH decreased (P < 0.01). We also found that survival of embryos significantly declined as acidification increased (P < 0.01). Behaviour of larval fish was significantly altered (P < 0.001) but not in a pH dependent manner. Our study suggests that weak acidification can cause negative effects to early life stage physiology and that behaviour can be altered. Our results suggest that if fish develop in weakly acidified freshwater there may be unfavourable impacts, including mortality at the most extreme levels.