Metals are ubiquitous in the environment. The aim of sustainable management of the agro-ecosystem includes ensuring that water continues to fulfill its function in agricultural production, cycling of elements, and as a habitat of numerous organisms. There is no doubt that the influence of large-scale irrigation projects has impacted the regional surface–groundwater interactions in the North China Plain (NCP). Given these concerns, the aim of this study is to evaluate the pollution, identify the sources of trace metals, analyze the influence of surface–groundwater interactions on trace metal distribution, and to propose urgent management strategies for trace metals in the agriculture area in China. Trace metals, hydrochemical indicators (EC, pH, concentrations of Na+, K+, Mg2+, Ca2+, Cl−, SO42−, and HCO3−) and stable isotopic composition (δ18O and δ2H) were determined for surface water (SW) and groundwater (GW) samples. Trace metals were detected in all samples. Concentrations of Fe, Se, B, Mn, and Zn in SW exceeded drinking water standards by 14.8%, 29.6%, 25.9%, 11.1%, and 14.8% higher, respectively, and by 3.8%, 23.1%, 11.5%, 11.5%, and 7.7% in GW. The pollution of trace metals in surface water was more serious than that in groundwater, and was also higher than in common irrigation areas in NCP. Trace metals were found to have a combined origin of geogenic and agriculture and industrial activities. Their distribution varied greatly and exhibited a certain relationship with the water flow direction, with the exception of a number of singular sites. Hydrochemical and environmental isotopic evidence indicates surface–groundwater interactions influence the spatial distribution of trace metal in the study area. Facing the ongoing serious pollution, management practices for source control, improved control technologies, and the construction of a monitoring net to warn of increased risk are urgently needed.