Soil microbiology examines the diverse microorganisms in soil, such as bacteria, fungi, algae, and protozoa, highlighting their critical role in maintaining soil fertility and soil health. These organisms contribute to nitrogen fixation, nutrient cycling, and reshaping soil structure, thereby improving plant growth and soil ecosystem. A notable aspect is the abundance of bacteria, with about 10 billion bacterial cells per gram of soil, showcasing their responsiveness to environmental changes. Additionally, the interaction between plants and root-associated microorganisms, particularly plant growth-promoting Rhizobacteria (PGPR), improves the availability of essential nutrients and enhances plant resilience, indicating their importance in sustainable agriculture and ecological health. Nature-based solutions (NBSs) in aquatic sediments provide sustainable methods for treating agricultural runoff and wastewater, particularly for nitrogen removal. These solutions, including constructed wetlands, buffer strips, planted canals, and aquatic sediment control ponds, utilize physical, chemical, and biological processes to reduce nitrogen levels in polluted water effectively. While the effectiveness of these systems has previously been documented, there are still key gaps in understanding the specific mechanisms and the factors involved that influenced their performance. Future research on enhancing the design and application of these systems can promote a circular economy by reusing treated wastewater for agricultural irrigation.