The inclusion of reclaimed effluents for irrigated agriculture may allow communities along the U.S.-Mexico border to use water resources more efficiently and reduce urban costs of wastewater treatment. However, metal inflow from industry and urbanization may threaten food safety. This study examines metal concentrations in sediments from open canal systems charged with flow from the Rio Grande and from effluents discharged from border communities. At the surface of canal beds, sediments were collected from six canal segments that began at the fringe of the El Paso/Juarez metroplex to rural areas downstream, and ranged from 9 to 24 km in length. Sediments were analyzed for Cd, Co, Cr, Cu, Ni, Pb, and Zn. These metals rarely exceeded 20 mg kg−1. Drainage and effluent conveyance increased the variability of metal concentrations in sediments. Geostatistical models did not significantly account for spatial variability of metals, except in Mexico. This may implicate multiple rather than single inflow sources of metals. Peaks in metal concentrations often coincided with growing rural communities. However, most metal concentrations were within conventional global ranges and were not at levels high enough to threaten food safety. Future sampling strategies will require reduced sampling intervals from 1 to <0.13 km.