AbstractThe causes of CO2 variations over the past million years remain poorly understood. Imbalances between the input of elements from rock weathering and their removal from the atmosphere‐ocean‐biosphere system to the lithosphere likely contributed to reconstructed changes. We employ the Bern3D model to investigate carbon‐climate responses to step‐changes in the weathering input of phosphorus, alkalinity, carbon, and carbon isotope ratio (δ13C) in simulations extending up to 600,000 years. CO2 and climate approach a new equilibrium within a few ten thousand years, whereas equilibrium is established after several hundred thousand years for δ13C. These timescales represent a challenge for the initialization of sediment‐enabled models and unintended drifts may be larger than forced signals in simulations of the last glacial–interglacial cycle. Changes in dissolved CO2 change isotopic fractionation during marine photosynthesis. This causes distinct spatio‐temporal perturbations in δ13C and affects the burial flux of 13C. We force a cost‐efficient emulator, based on the Bern3D results, with contrasting literature‐based weathering histories over the last 800 thousand years. Glacial–interglacial amplitudes of up to 30 ppm in CO2, 0.05‰ in δ13C, and ∼15 mmol m−3 in deep ocean are emulated for changes in carbonate rock weathering. Plausible input from the decomposition of organic matter on shelves causes variations of up to 10 ppm in CO2, 0.09‰ in δ13C, and 5 mmol m−3 in , highlighting the non‐negligible effect of weathering‐burial imbalances.