For species exhibiting parental care, the way in which parents adjust care behaviour to compensate for environmental change potentially influences offspring survival and, ultimately, population viability. Using the three-spined stickleback (Gasterosteus aculeatus) – a species in which males provide parental care by building and tending a nest and fanning the eggs – we examined how low dissolved oxygen (DO) levels affect paternal care, embryo development and survival. Although levels of nest tending were unaffected by DO level, we found that larger males fanned their embryos more under low oxygen conditions. This resulted in faster rates of embryo development within the clutches of these larger males, but reduced embryo survival at 7 days post-fertilization compared to clutches of smaller males. Our results suggest that although parents may attempt to compensate for environmental change via alterations to care behaviour, their ability to do so can be dependent on parental phenotype. This sets up the potential for oxygen levels to act on the strength and direction of selection within populations. We discuss possible explanations for the surprising result that supposedly adaptive changes in care behaviour by large males (i.e. increased fanning) led to reduced embryo survival at 7 days post-fertilization, and whether, as a consequence, acute environmental conditions may have the potential to overwhelm selection on sexual traits.