Accelerated urban development has led to high levels of untreated sewage (containing nitrogen) entering aquatic ecosystems directly, which makes nitrogen (N) become ubiquitous pollutants in the water environment across the world. Excessive N loading in rivers can cause deterioration of water quality and lead to direct input into riparian aquifers. To meet the N demand of riparian crops, excessive fertilizers (natural (manure) and synthetic fertilizers) were applicated, combined with the irrigation of polluted river water, which also resulted in significantly increasing N concentration in riparian groundwater, especially in the agricultural watershed. These both may raise the degradation issues of riparian ecosystems. To develop effective nitrogen pollution mitigation strategies and achieve water resource sustainability, it is critical to understand the N sources and transformation in the riparian groundwater of polluted rivers. However, the environmental characteristics in the riparian zones have been drastically changed between the groundwater and surface water (GW-SW) interaction, which results in distinct physical, chemical and biological gradients. It is more challenging to explore N source and transformation in riparian groundwater. The study area (the Shaying River Basin) located in Eastern China, is a highly regulated and heavily N (nitrogen) polluted catchment. Due to intensive urbanization and industrialization in recent decades, huge manure and wastewater discharges (high Nitrogen contents) into the Shaying River, resulting in the deterioration of the river quality. The river level and velocity have been strongly regulated by several sluices since the 1960s, and the frequent operation of sluices has further deteriorated river pollution. This phenomenon is typical in the midstream of the Shaying River. The polluted river water directly affected the N level in riparian groundwater through riparian leakage. N pollutants stored in the aquifers could also become the potential second contaminant source to river systems. Furthermore, the fluctuations of groundwater-surface water interaction driven by sluices regulation will influence the N sources and N cycle mechanism, particularly those related to N-loss (e.g. denitrification, anammox and DNRA) or gains (vertical leaching) on both spatial and temporal scales in the riparian groundwater. However, no systematic study has been conducted to date in this study area. Given this background, two-year field observations (rainfall and water level), survey sampling (river, groundwater and rainwater) and indoor experiments (hydrochemistry, nitrogen species, 11 isotopes and microorganisms) were used in this research and the aim was reined into the following objectives: (i) identify water environment characteristics in the riparian zone of the main tributaries in the Shaying River Basin (Chapter 2); (ii) on this basis, we constructed two long-term monitoring transects (ZK and HD) to study the hydrodynamic characteristics in the riparian zone of the midstream (Chapter 3); (iii) furthermore, quantitatively estimate the contribution of nitrate source and investigate how processes identified in objectives (ii) affect the nitrogen transformation mechanisms in riparian zones (Chapter 4). The main conclusions are as follows: (1) Untreated sewage discharge and fertilizer usage were the main anthropogenic activities affecting the water environment in river and riparian groundwater of Shaying River Basin. Nitrogen pollution in rivers and groundwater is serious in the midstream of Shaying River. Nitrate pollutants derived from riparian groundwater were potential threats to river quality at the lower reaches of Jialu River and Shenqiu county of Shaying River, where the nitrate inputs could be larger during the wet seasons because of higher groundwater discharge. (2) A decrease in the river level occurred during the flood season due to sluice regulation, resulting in riparian groundwater discharged into the river. Furthermore, as the distance from the river increased, temperature (T), pH and stable isotopes (δ18O and δD) concentrations decreased, whereas the EC and 222Rn concentrations increased. Microbial community structures in near-river wells were comparable to that in the river, indicating the mixing process of the river water with the riparian GW. According to the results of the linear mixing model, the extent of GW-SW interaction was quantitatively to be within 72 and 32 m from the river at the ZK and HD transect, respectively. The residence time in riparian GW ranged from 0.32 to 8.68 days and 3.03 to 15.00 days, respectively at the ZK and HD transect. River leakage was found to be equal to 1.43×10-3 m3/(s·m)-3.77×10-4 m3/(s·m) at the ZK transect whilst groundwater discharge was 4.17×10-2 m3/(s·m) - 2.54×10-2 m3/(s·m) at the HD transect. (3) River (TN: 2.33 mg/L (ZK) and 5.25 mg/L (HD)) and riparian groundwater (TN: 0.42-6.61 mg/L (ZK) and 2.41-24.46 mg/L (HD)) are seriously suffered from N contaminated (mainly in forms of NO3--N) at two monitoring transects in the midstream of the Shaying River. Sewage and manure were the main sources of nitrate (ZK: 73.15±6.95%; HD: 77.80±13.40%) in rivers and riparian groundwater during the sampling period. Overall, the key controlling factors for riparian N concentration included mixing/dilution effects with river/rainwater, external N input and biochemical process (including nitrification, denitrification and anammox). Nitrogen can be removed by aerobic denitrification (mainly) and anammox at the river-groundwater interface and the absolute amount of NO3- being removed is positively related to FRiver, substrate concentration (NO3-) and microorganisms. Fertilization management and wastewater discharge control were important to reduce nitrogen pollution in the riparian zone of Shaying River.