Gyrolithes burrows reflect fluctuating salinity in incised valleys that were filling when estuarine circulation was established during Holocene transgression in a mesotidal setting off southern Vietnam. Gyrolithes burrows were produced in stiff mud, but they postdate burrows with diffuse outlines formed in soft mud, and they predate burrows of the Glossifungites suite that represent fully marine conditions. The latter are filled with and overlain by marine sand and shell debris deposits. The pore-water composition of the Gyrolithes host sediment supports these findings while exhibiting only 75%–95% of marine chloride values. Gyrolithes is restricted to low-gradient parts of the inner shelf. In narrow confined valleys, an estuarine circulation was established and a temporally lengthy omission ensued while fluvial and tidal currents interacted. The absence of Gyrolithes in other parts of the study area is explained by the steep gradient of incised valleys. This might have resulted in accelerated currents in the incised valleys precluding the Gyrolithes trace maker. Alternatively, environmental conditions resulting from rapid sea-level rise, including increased mud deposition, might have been unfavorable for Gyrolithes producers. No Gyrolithes burrows were found in areas where normally thin marine transgressive deposits rest directly on Pleistocene paleosols.