Preservation bias may significantly impact the application of detrital zircon geochronology in reconstructing Earth surface processes. Here we compare detrital zircons from the actively eroding Murchison River channel in Western Australia with Ordovician fluvial sediments that have drained similar source rocks along the western margin of the West Australian Craton. In addition to standard analysis of detrital zircon age spectra we apply multivariate statistics to test the relation between 3-D grain shape, U-content and U–Pb ages, with the objective to quantify differences between both sample groups and track preservation along the transport pathway of the Murchison River. Our results show that zircon grains in modern river sands display an upstream trend toward larger surface areas, volume equivalent diameters and grain widths, as well as toward higher U-contents and lower apparent grain densities. 3-D grain shape, size and age spectra of Murchison River zircons evolve consistently downstream, but even at the river outlet remain distinct from the Ordovician samples, as a less mature representation of source. We interpret Ordovician river zircons to represent a significantly depleted subset from which up to 22% of the zircon population may have been lost compared to the actively transported detrital load. This discrepancy between the characteristics of detrital zircons in modern active rivers and ancient fluvial Ordovician sandstones demonstrates a bias that could be relevant for other source-sink detrital transport systems throughout Earth history.