[3] The defining feature of Hydropunctaria is its frequent development of carbonaceous structures within the thallus, which appear punctiform to columnar and can originate from an often rough and uneven involucrellum.

Documented thallus colours include yellowish-brown, green, and dark grayish olive to black.

The uppermost layer of cortical cells, when present, often contain yellowish to brown or olive-blackish pigments; this characteristic, however, is not always consistent, as evidenced by the colourless specimens sometimes collected from shaded sites.

The layer of algal cells is not clearly differentiated from the upper cortex, although generally they are usually arranged in vertical columns, occasionally interrupted by black punctae.

The excipulum (the cup-shaped layer of tissue surrounding the hymenium) is either pale with a brown ostiole or completely pigmented.