Rhynia gwynne-vaughanii is a primitive vascular plant with branching leafless stems that reached a height of about 18 cm and culminated in fusiform sporangia. The upright stems branched from creeping branching horizontal rhizomes that bore delicate hair-like roots. The lateral branches could overtop the sporangia-bearing stems, and the upright portions of the plant would have had a thicket-like appearance. Small bumps along the stems may contain archegonia, which indicate a possible bryophyte-like life history, although this is still unclear. But there is also a distinct protostele composed of distinct phloem and only a handful of xylem cells.
The species is commonly present as monotypic stands, and seems to have been an early colonizer of well-drained sinter (hot spring sedimentary deposits) and sandy substrates. It is also found associated with all other Rhynie plants except (apart from very rarely) Horneophyton, suggesting that Rhynia was a vigorous, perhaps weed-like, form tolerant of a wide range of habitats and able to withstand interspecies competition within the Early Devonian ecosystem.