The San Juan River is a major water source for communities in the Four Corners region of the United States (parts of Colorado, Arizona, New Mexico, Utah) and is a vital source of water for the Navajo Nation. The Navajo Nation Environmental Protection Agency (NNEPA) periodically samples surface water on the Navajo Nation and has found that some elements exceed NNEPA surface water standards (the upper limits of an element for consumption or other use of water). Constituents of concern are substances that could be harmful if present in sufficient quantities, and it is important to monitor the concentrations of these substances in the environment. In the San Juan River, constituents of concern include metals detected in river water, such as arsenic, lead, and aluminum. These metals can come from natural sources or can result from anthropogenic (human) activities and can affect the health of people, plants, and animals. The U.S. Geological Survey (USGS) is working with the NNEPA to identify sources of metals and trace elements entering the San Juan River from tributaries in the reach flowing through the Navajo Nation, and to quantify the contribution from each natural and human-caused source. Sediments were collected in sediment traps in 33 ephemeral or perennial channels that flow into the San Juan River. The sediment traps were placed in the apparent thalweg of the channel, and attached to a T-post. Sites were checked every 2 to 3 weeks and sediment traps were collected if material accumulated. If the traps were empty, they were left deployed. The sediment traps filled during storm events. This data release contains sediment electron microscopy back scatter images and energy-dispersive X-ray spectroscopy (EDS) spectra to identify general chemistry, mineralogy, and grain size from sediments mobilized during high-flow events in the tributaries to the San Juan River. Images and EDS spectra from four locations at 33 sample sites and a sample database file are included. The database file includes the name of each site, names of associated images, grain size and rounding, and elements identified in each image. Images are provided in .zip folders by sample location.