Manayunkia aestuarina is a small, colourless or brown, sabellid fanworm reaching up to 6 mm in length. Eight yellow ciliated tentacles (pinnules) and two green ciliated palps project from the head of the worm. The mouth is located beneath the palps and there is a black eye spot either side of the head (prostomium). The rest of the body comprises eight thoracic and three abdominal segments. Bristles on the thoracic segments are lance-like and short. Manayunkia aestuarina bind sand and mud particles together to form a tube roughly twice the length of the animal.