Geochemical studies of lake sediment from Eagle Rock Lake and upper Fawn Lake were conducted to evaluate the effect of mining at the Molycorp Questa porphyry molybdenum deposit located immediately north of the Red River. Two cores were taken, one from each lake near the outlet where the sediment was thinnest, and they were sampled at 1-cm intervals to provide geochemical data at less than 1-year resolution. Samples from the core intervals were digested and analyzed for 34 elements using ICP–AES (inductively coupled plasma–atomic emission spectrometry). The activity of ¹³⁷Cs has been used to establish the beginning of sedimentation in the two lakes. Correlation of the geochemistry of heavy-mineral suites in the cores from both Fawn and Eagle Rock Lakes has been used to develop a sedimentation model to date the intervals sampled. The core from upper Fawn Lake, located upstream of the deposit, provided an annual sedimentary record of the geochemical baseline for material being transported in the Red River, whereas the core from Eagle Rock Lake, located downstream of the deposit, provided an annual record of the effect of mining at the Questa mine on the sediment in the Red River. Abrupt changes in the concentrations of many lithophile and deposit-related metals occur in the middle of the Eagle Rock Lake core, which we correlate with the major flood-of-record recorded at the Questa gage at Eagle Rock Lake in 1979. Sediment from the Red River collected at low flow in 2002 is a poor match for the geochemical data from the sediment core in Eagle Rock Lake. The change in sediment geochemistry in Eagle Rock Lake in the post-1979 interval is dramatic and requires that a new source of sediment be identified that has substantially different geochemistry from that in the pre-1979 core interval. Loss of mill tailings from pipeline breaks are most likely responsible for some of the spikes in trace-element concentrations in the Eagle Rock Lake core. Enrichment of Al₂O₃, Cu, and Zn occurred as a result of chemical precipitation of these metals from ground water upstream in the Red River. Comparisons of the geochemistry of the post-1979 sediment core with both mine wastes and with premining sediment from the vicinity of the Questa mine indicate that both are possible sources for this new component of sediment. Existing data have not resolved this enigma.