The interaction between groundwater and surface water (GW-SW) affects the hydrogeochemical cycle, leading to changes in nitrate sources, migration, and transformation within watersheds. Seasonal freeze-thaw cycles also complicate the above processes. This study employed hydrochemistry, stable isotope analysis, and statistical methods to investigate the dynamic characteristics of GW-SW exchange in a seasonal freeze-thaw watershed, identify the conversion intensities during different periods, and elucidate potential nitrate sources and their relative biogeochemical processes. GW and SW were replenished primarily by atmospheric precipitation, which switched to snowmelt water during the thawing period. Recharge sources and aquifer lithology controlled the seasonal variation in GW-SW exchange. From upstream to downstream, the conversion intensity ranges of SW loss into GW during the wet period were 54.6%, 32.7-55.5%, and 26.5-37.4%, respectively. The percentages of streams that gained GW during the dry period were 62.2-83.7%, 47.1-62.0%, and 35.2-46.0%, respectively. The primary sources of nitrate in GW and SW were fertilizers and livestock waste, with their contributions exhibiting seasonal variations with GW-SW interactions. Agricultural activities and livestock breeding led to high nitrate contents in groundwater, with manure and sewage accounting for up to 90% of the nitrate content during the dry period. Notably, GW-SW interactions during the wet and dry seasons enhanced the denitrification process, contributing to nitrate removal in groundwater. This study revealed that GW-SW interactions significantly impact the fate of nitrate in watersheds and the influence of human activities on watershed environments, providing technical support for watershed water resource management and diffuse pollution control.