Improving our ability to predict when and how biodiversity mediates ecosystem processes requires greater consideration of how different dimensions of biodiversity, such as species‐specific physiology or behaviour, can independently and interactively affect these processes. Global change drivers, such as increased temperature, can also alter organismal metabolism in ways that may interact with different dimensions of biodiversity, further reducing predictability. Using an individual‐based model of a seagrass‐patch reef ecosystem, we quantified (1) how species‐level physiological traits of two common reef fish, (2) foraging behaviours and (3) increasing water temperatures interacted to affect ecosystem‐level primary production (PP) via consumer nutrient excretion. At ambient temperature, physiology more strongly regulated ecosystem PP than behaviour, which primarily influenced where PP occurred. Increased temperature strongly independently resulted in greater ecosystem PP until a threshold whereafter ecosystem PP drastically decreased for both fish species. Temperature strongly interacted with physiology to non‐additively increase ecosystem PP but only weakly interacted with behaviour due to underlying metabolic mechanisms. Our study highlights the importance of species‐level physiology for regulating ecological processes and that increased temperatures will alter biodiversity‐ecosystem process relationships in unpredictable ways. Importantly, because we quantified both the direct effects of physiology and behaviour on nutrient supply via excretion and the indirect effects of this on primary production, we were able to determine that quantifying consumer‐mediated nutrient supply alone was insufficient to predict ecosystem‐scale primary production. Our findings emphasize that understanding the mechanisms by which biodiversity affects ecosystems requires quantifying ecosystem‐scale responses, which also places findings at scales relevant for conservation.