The linkages of distributed ponds are utilized in conjunction with one another to remediate non-point source (NPS) pollution in a water-scarce basin. This study provides an overview of a state-of-the-art thorough evaluation of ponds, which offers insight into the majority of topics covered by the ongoing scientific studies, including their various functions and factors affecting their functioning on the hydrological, physicochemical, and biological processes, such as environmental climate factors and basin-specific landscape configuration parameters, as well as process parameters for design, operation and management aspects. The linkages of ponds provide a variety of sustainable services (6R functions), such as resources, restoration, reduction, reuse, recycling, and recovery. The significance of regional environmental geochemical substrates in the ponds, such as red soil, as a hotspot for microbial reaction is emphasized to demonstrate the significant contribution of the migration and transformation of Fe/N cycles to the pollution removal process. In this review, 178 original research publications were thoroughly analyzed to improve our knowledge of the iron-nitrogen cycle in wetlands. From a molecular biology standpoint, the identification of functional microbe species and genes linked to microbially driven iron-nitrogen cycle activities is delved. Reliable data and homogeneous datasets from 42 studies were collected. The correlation analysis results demonstrated Feammox rates contributed to the N loss amount (r = 0.871
p <
0.01), and they had a positive correlation with Fe(III) concentration (r = 0.965
p <
0.01). The proposal for the treatment of NPS pollution by large-scale linkages of ponds in a basin involves optimizing Fe/N microbial processes to promote iron crystallization and efficient circulation of Fe(II) and Fe(III). The co-benefits of geochemistry, biotechnology, and environmental science should be considered when managing contamination in engineering applications. The linkages framework for integrated ponds, which incorporates macro (watershed management) and micro (biogeochemical cycle mechanism) investigations, provides a systematic approach to the application of integrated ponds and sustainable water management for NPS pollution control.