Seabirds play a vital role in marine ecosystems and the long-term study of their responses to environmental variations can be used to monitor the effects of climate change on marine fauna. However, slight differences in similar seabird species result in a range of responses which complicates our understanding of the effects of environmental changes to marine ecosystems. The present study investigated inter-annual differences in the breeding biology (breeding phenology, chick growth rates and breeding success) and environmental conditions (seasonal sea surface temperatures) of important foraging areas in two sympatric small Procellariiform species, the fairy prion ( Pachyptila turtur ) and the common diving petrel ( Pelecanoides urinatrix ), over four reproductive seasons (2017–2020) in Bass Strait, south-eastern Australia. Marine heatwaves occurred during the years of 2018/19 and 2019/20 and coincided with years of delayed laying dates, slower chick growth and reduced breeding success, in both species. While fairy prions maintained a relatively high breeding success and broadly constant breeding phenology, common diving petrels delayed the start of the breeding season by up to 50 days and experienced dramatic collapses in breeding success in years of high marine heat wave occurrence. The difference in foraging ecology and physiological capacity (largely in the production of stomach oils and fasting abilities of adults and chicks) between both species are likely to influence the variability and phenology in the observed breeding seasons.