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Nutrients, such as nitrogen and phosphorus, provide vital support for human life, but overloading nutrients to the Earth system leads to environmental concerns, such as water and air pollution on local scales and climate change on the global scale. With an urgent need to feed the world's growing population and the growing concern over nutrient pollution and climate change, sustainable nutrient management has become a major challenge for this century. To address this challenge, the growing body of research on nutrient budgets, namely the nutrient inputs and outputs of a given system, has provided great opportunities for improving scientific knowledge of the complex nutrient cycles in the coupled human and natural systems. This knowledge can help inform stakeholders, such as farmers, consumers, and policy makers, on their decisions related to nutrient management. This paper systematically reviews major challenges, as well as opportunities, in defining, quantifying, and applying nutrient budgets. Nutrient budgets have been defined for various systems with different research or application purposes, but the lack of consistency in the system definition and its budget terms has hindered intercomparison among studies and experience‐sharing among researchers and regions. Our review synthesizes existing nutrient budgets under a framework with five systems (i.e.,Soil‐Plantsystem,Animalsystem,Animal‐Plant‐Soilsystem,Agro‐Foodsystem, andLandscapesystem) and four spatial scales (i.e., Plot and Farm, Watershed, National, and Global scales). We define these systems and identify issues of nitrogen and phosphorus budgets within each. Few nutrient budgets have been well balanced at any scale, due to the large uncertainties in the quantification of several major budget terms. The type and level of challenges vary across spatial scales and also differ among nutrients. Improvement in nutrient budgets will rely not only on the technological advancement of scientific observations and models but also on better bookkeeping of human activity data. While some nutrient budget terms may need decades, or even centuries, of research to be well quantified within desirable levels of uncertainties, it is imperative to effectively communicate to interested stakeholders our understanding of nutrient budgets so that scientists and a variety of stakeholders can work together to address the sustainable nutrient management challenge of this century.