Nutrient inputs from the atmosphere and rivers to the ocean are increased substantially by human activities. However, the effects of increased nutrient inputs are not included in the widely used CMIP5 Earth system models, which introduce bias into model simulations of ocean biogeochemistry. Here, using historical simulations by an Earth system model with perturbed atmospheric and riverine nutrient inputs, we show that the contribution of anthropogenic nutrient inputs to past global changes in ocean biogeochemistry is of similar magnitude to the effect of climate change. Anthropogenic nutrient inputs increase oceanic productivity and carbon uptake, offsetting climate-induced decrease and accelerating climate-driven deoxygenation in the upper ocean. Moreover, accounting for anthropogenic nutrient inputs improves the known carbon budget imbalance and model underestimation of the observed decrease in the global oxygen inventory. Considering the effects of both nutrient inputs and climate change is crucial in assessing anthropogenic impacts on ocean biogeochemistry.