The Lunpola Basin in central Tibet is a Cenozoic lacustrine rift basin with widespread organic‐rich shale and oil shale depositions. Forty‐nine samples were collected from the Lunpola section to evaluate the controlling factors of trace‐element enrichment and mineralogical composition in the lacustrine rift basin. Minerals identified in the Lunpola section include abundant quartz, calcite, and clay minerals; minor quantities of feldspar, dolomite, siderite, and mirabilite; and trace amounts of aragonite, magnesite, salt, pyrite, hematite, zeolite, barite, amphibole, gypsum, anhydrite, anatase, galena, sphalerite, apatite, chromite, zircon, and monazite. The Lunpola shale and oil shale are enriched in trace elements B, Cr, Ni, Mo, and U, in comparison to the upper continental crust. Three processes were probably responsible for the geochemical anomalies found in the Lunpola Basin, including the detrital material input, lake water, and hydrothermal activities. Mineralogical and geochemical data show that the lake water is the dominant influences on the elevated trace element concentrations in the shale and oil shale. The depletion or enrichment of trace elements in sediments from the lacustrine rift basin is governed by general processes (e.g. anoxic environment). Additionally, hydrothermal fluids also cause remobilization of some trace elements in the Lunpola lacustrine rift basin. Copyright © 2017 John Wiley & Sons, Ltd.