In order to reveal the migration and transformation process of nitrogen and phosphorus in groundwater in the hyporheic zone of wetland, the wetland near the entrance of the Xiang River to Dongting Lake was taken as the study area, and surface water and groundwater samples were collected and hydrochemical parameters were measured periodically. The entropy weight index method was used for water quality evaluation, and correlation analysis and structural equation modeling were applied to study the driving mechanism of physicochemical parameters on nitrogen and phosphorus migration and transformation. The results show that 58.8% of the groundwater samples are class IV or V, and total nitrogen (TN), NH+4 and total phosphorus (TP) are the main overstandard factors. The migration and transformation of nitrogen are mainly controlled by mineralization, denitrification, and dissimilatory nitrate reduction to ammonium, and the migration and enrichment of phosphorus are closely related to the reducing dissolution of Fe/Mn oxides or hydroxides. The contents of nitrogen and phosphorus components in the groundwater show obvious differences between the wet and the dry seasons. Under the influence of the hyporheic exchange, except for NH+4, dissolved organic nitrogen and TN, the contents of NO-2,NO-3, TP and soluble reactive phosphorus in the groundwater decrease with increasing distance from the riverbank. Temperature, redox potential, dissolved oxygen, total dissolved solids, and electrical conductivity can affect microbial activity and are key driving factors for nitrogen and phosphorus migration and transformation in groundwater.