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Soil nutrient mining is on-going in Bangladesh and, thus, is impairing major food production in many cases. Understanding plant–soil–nutrient interactions in various agro-ecosystems is essential for sustainable crop production, especially rice grains, the staple food of approximately 156 million people from the country. This chapter addresses soil fertility management options for increasing rice production in relation to nutrient balance and mining in rice-based cropping systems. The soil fertility status of Bangladesh varies widely in different regions. There are multiple nutrient deficiencies in most cases and recommendations by different organizations are either inadequate or farmers are not following them. Besides, long-term trials reveal that only inorganic nutrient sources are not adequate to sustain rice production in Bangladesh. Heavy metal contamination, changes in electrical conductivity because of industrial wastes, lowering of pH, arsenic contamination, etc., are responsible for stress in crop growing environments along with biotic and abiotic stress. Rapid carbon mineralization because of the hot and humid climate of the country is also playing an important yet negative role in rice soil health. Supplementing nutrients for rice crops in integrated ways is essential in managing soil fertility and production sustainably.