It can be readily distinguished from another southern African pipefish with which it shares its habitat, S. temminckii, by its much shorter snout.

The estuarine pipefish is most commonly found in beds of the eelgrass Zostera capensis.

[2] The estuarine pipefish was declared extinct in 1994, but was rediscovered in 2006[3] in areas where it had not been reported in over four decades.

This pipefish is Critically Endangered due to both natural and human threats to the brackish estuaries and local eelgrass beds in which it lives.

[1] A captive population of Syngnathus watermeyeri is held at uShaka Marine World in Durban.