Abstract Numerical simulations using a physiologically-based model of marine ecosystem size spectrum are conducted to study the influence of primary production and temperature on energy flux through marine ecosystems. In stable environmental conditions, the model converges toward a stationary linear log–log size-spectrum. In very productive ecosystems, the model predicts that small size classes are depleted by predation, leading to a curved size-spectrum. It is shown that the absolute level of primary production does not affect the slope of the stationary size-spectrum but has a nonlinear effect on its intercept and hence on the total biomass of consumer organisms (the carrying capacity). Three domains are distinguished: at low primary production, total biomass is independent from production changes because loss processes dominate dissipative processes (biological work); at high production, ecosystem biomass is proportional to primary production because dissipation dominates losses; an intermediate transition domain characterizes mid-production ecosystems. Our results enlighten the paradox of the very high ecosystem biomass/primary production ratios which are observed in poor oceanic regions. Thus, maximal dissipation (least action and low ecosystem biomass/primary production ratios) is reached at high primary production levels when the ecosystem is efficient in transferring energy from small sizes to large sizes. Conversely, least dissipation (most action and high ecosystem biomass/primary production ratios) characterizes the simulated ecosystem at low primary production levels when it is not efficient in dissipating energy. Increasing temperature causes enhanced predation mortality and decreases the intercept of the stationary size spectrum, i.e., the total ecosystem biomass. Total biomass varies as the inverse of the Arrhenius coefficient in the loss domain. This approximation is no longer true in the dissipation domain where nonlinear dissipation processes dominate over linear loss processes. Our results suggest that in a global warming context, at constant primary production, a 2–4 °C warming would lead to a 20–43% decrease of ecosystem biomass in oligotrophic regions and to a 15–32% decrease of biomass in eutrophic regions. Oscillations of primary production or temperature induce waves which propagate along the size-spectrum and which amplify until a “resonant range” which depends on the period of the environmental oscillations. Small organisms oscillate in phase with producers and are bottom-up controlled by primary production oscillations. In the “resonant range”, prey and predators oscillate out of phase with alternating periods of top-down and bottom-up controls. Large organisms are not influenced by bottom-up effects of high frequency phytoplankton variability or by oscillations of temperature.