The Tia Juana River Estuary is located in the portion of the Tia Juana River flood plain north of the United States-Mexico border, known as the Lower Tia Juana River Valley. The opening of the estuary to the Pacific Ocean is 1.5 km north of the international border. The estuary is composed of a series of narrow tidal channels which radiate from a restricted opening to the ocean in northerly, southerly, and easterly directions. The Tia Juana River flows in a westward direction and empties into the central portion of the estuary. Five sediment cores were taken, four from different tidal channels within the estuary and one from the Tia Juana River. Anthropogenic inputs were found for the following metals in all four tidal channels: Pb, Zn, Cu, and Ni. Low anthropogenic levels were detected for Fe and Cd in several of the tidal channels. The upper portion of each tidal channel has an organic-rich black silt layer thought to be related to increased population and industrialization within and adjacent to the Tia Juana River Drainage Basin within the last few decades. It is in this region that the above-mentioned metals reach their highest values. Mn is apparently mobile in this region and may possibly scavenge some of the Pb, Zn, and Co as it migrates to more oxidizing conditions, possibly forming an Mn carbonate. Compared to other sediments associated with water systems near industrialized-urbanized areas of California and the eastern United States, the Tia Juana estuarine sediments are less polluted. No specific point sources could be identified for the anthropogenic metal inputs to the Tia Juana Estuary. Possible sources include: (1) urban runoff within the Tia Juana River flood plain during storms, (2) raw sewage, derived mainly from the city of Tijuana, entering the estuary via the Tia Juana River, (3) deposition of airborne particulates related to burning of fossil fuels, and (4) automobile traffic.