Integrated nutrient management systems that use a holistic approach, using inorganic fertilizers as well as management practices aimed to increase soil organic matter, are needed to improve soil health. Management practices need to take into account differences in soil properties, climate and available local resources. In this chapter, we discuss the chemistry of nutrients focusing mostly on nitrogen and phosphorus. The impact of chemical composition of soils (nutrients, pH and salinity) on soil health is discussed. We review factors influencing the solubility of nutrients and discuss management practices to improve nutrient availability and reduce the reliance on inorganic fertilizers. We illustrate a case study from India that shows how integrated nutrient management, using both inorganic fertilizers, including sulphur and micronutrients, and practices to improve and increase soil organic carbon, can be done successfully and used on a large scale using site-specific research and available resources.