The Paleozoic evolution of vegetation transformed terrestrial landscapes, facilitating novel sedimentary processes and creating new habitats. This transformation left a permanent mark on the sedimentary record, perhaps most strikingly via an upsurge in preserved terrestrial mudrock. Whereas feedbacks between evolving vegetation and river structure have been widely studied, Paleozoic estuaries have so far received scant attention. Located at the interface between the land and sea, the co-adjustment of estuarine morphology and plant traits are fundamentally tied to a varied range of geochemical cycles, and determine how global silicate weathering patterns may have varied over time. Here we employ an eco-morphodynamic model with an in-built vegetation code to simulate estuarine morphology through five key stages in plant evolution. An abiotic model (early Precambrian?) saw mud deposition restricted to fortuitous instances of limited erosion along bar-flanks. Estuaries colonized by microbial mats (Precambrian onwards) facilitated mud accretion that sufficiently stabilized bar surfaces to promote extensive mudflat development. Small-stature, rootless vegetation (Silurian–Early Devonian) introduced novel above-ground baffling effects which led to notable mud accumulation in lower-energy environments. The incorporation of roots (Early Devonian) strengthened these trends, with root structures decreasing the mortality of the occupying plants. Once the full complement of modern vascular plant architectures had evolved (Middle Devonian), dense colonization promoted the formation of in-channel islands accompanied with system-wide mud accumulation. These simulations suggest estuaries underwent profound change during the Paleozoic, with the greening of the continents triggering processes and feedbacks which render all previous source-to-sink sediment pathways non-uniformitarian.