Of very limited distribution, it is known to survive only as one population in seasonal pools over granite near Stellenbosch, where it is threatened by the encroachment of alien species and eutrophication from the sewage works on whose grounds it grows.

The leaves widen at their base to about 4 millimetres (0.2 in) wide to accommodate sporangia, and bear a narrow wing of membranous-textured tissue at their margins there.

[2] While several other species of South African Isoetes also have reticulate megaspores, I. stellenbossiensis and I. wormaldii have much more uniform ridges and smaller areoles between them than those of I. stephanseniae.

[2] Of the two populations known, one was destroyed by the expansion of Stellenbosch University; the remaining one is protected on the grounds of the local sewerage works.

[2] During the summer, the pools and marshlands where the species occurs dry up, and it becomes dormant, with the pseudocorm waiting until the first rain to put up new leaves.