Sediment transport through the Mississippi River affects the lives and economies of millions of people along its course, so that understanding the controls on this process is of scientific and societal importance. Detrital U‐Pb geochronology, supported by grain size and major element data, can be a robust tool for constraining sediment provenance in clastic sedimentary systems that has been applied to the Mississippi. However, sediment storage and reworking can complicate interpretation, and this can be further exacerbated by anthropogenic alteration via the construction of levees, dams, locks and river diversion projects. In this study, we date zircons from the modern Mississippi River and compare them to previously acquired data to illustrate the difference between samples taken from the same catchment in order to better understand the downstream propagation of the modern detrital zircon signal. The modern Mississippi River and tributary systems show distinct similarities and are comparable between studies when samples are not too far separated (<100 km). We estimate that the Arkansas River is more important than previously proposed, at least in terms of sand supply, supplying 7%–11% of the total load. The largest supplier of sediment to the Mississippi is the Missouri River (33%–43%), which derives much of its sediment from sedimentary rocks in the foredeep deposited during the Sevier and Laramide events. Anthropogenic alteration of the modern river system can be seen in the downstream propagation of a Red River cut‐off signal following construction of the “River Control Structure”, implying slow zircon transport rates (<2.8 km/year). Differences in the degree of recycling caused by sampling locations and low numbers of grains introduce significant uncertainties to mixing calculations.