Understanding the response of marine organisms to temperature is crucial for predicting climate change impacts. Fundamental physiological thermal performance curves (TPCs), determined under controlled conditions, are commonly used to project future species spatial distributions or physiological performances. Yet, real‐world performances may deviate due to extrinsic factors covarying with temperature (food, oxygen, etc.). Using a bioenergetic marine ecosystem model, we evaluate the differences between fundamental and realised TPCs for fish species with contrasted ecology and thermal preferences. Food limitation is the primary cause of differences, decreasing throughout ontogeny and across trophic levels due to spatio‐temporal variability of low‐trophic level prey availability with temperature. Deoxygenation has moderate impact, despite increasing during ontogeny. This highlights the lower sensitivity of early life stages to hypoxia, which is mechanistically explained by lower mass‐specific ingestion at older stages. Understanding the emergence of realised thermal niches offers crucial insights to better determine population's persistence under climate warming.