It predominantly resides in darkly stained tannic waters in the lower levels of lentic ecosystems, although may be found in clearwater swamps, and feeds on fish larvae, eggs, but more often small invertebrates.

It prefers areas with mudbeds and dense vegetation, and has a remarkable tolerance for low oxygen levels.

Although many populations are found, the range is limited, and suitable habitat is easily lost to development.

Females will become noticeably fatter, while males will darken and begin to move into their spawning territories.

[6] Where their ranges overlap, the spawning coloration of the three-spined stickleback is black, similarly to male Olympic mudminnows.