Isoetes microvela is endemic to North Carolina, U.S.A., on the Atlantic Coastal Plain, where it is restricted to blackwater river systems. Flooding related to hurricanes and heavy rain is the greatest threat to the species and could severely diminish the global population in any one major storm event. The species occurrences are spread across four watersheds (locations) that may respond uniquely to flooding events. Climate change is likely to increase the frequency of these events. This species meets the requirements for Endangered under criterion B for area (EOO <5,000 km², AOO <500 km²), a continuing decline in the number of mature individuals and the quality of habitat, and number of locations (≤5).

Isoetes microvela is endemic to the Atlantic Coastal Plain of North Carolina, U.S.A. It is known from six to seven populations along the North Carolina coast.

Flooding after a hurricane significantly reduced the largest known population in the mid-1990s. It is not known if the species has recovered at this site. Flooding due to heavy rain and hurricanes has altered the shorelines of potential habitat; surveys targeting the species have been largely unsuccessful (B. Wichmann pers. comm. 2020).

This species occurs in Blackwater River Systems, permanent water courses under the deep shade of deciduous swamp forests. It grows in sandy alluvium, usually with little or no associated vascular vegetation in shallow water or on seasonally exposed streambanks where it can be severely impacted by storm-induced flooding. At least one site is on a rare calcareous substrate in the vicinity of a number of other rare Coastal Plain endemic species (Brunton and Britton 1998).

Flooding related to hurricanes caused population declines in 1996 and 1997. Future flooding events due to heavy rain or hurricanes, which are likely to be more prevalent with climate change, could cause similar or more pervasive declines (B. Wichmann and W. Knapp pers. comm. 2020). Campground activities are a threat at one site.

One occurrence is in a state natural area.