Species of organisms introduced in otherwise stable ecosystems upset the natural ecological balance of water and shorelines. They have few predators or competitors to control their populations. This province is vulnerable to invaders, due to the manner in which water drains into Saskatchewan from other regions.

Several invader species may threaten fish habitat; from shelled molluscs to aquatic plants. The more obvious of invaders include fish species which, once introduced, compete directly with native fish for food and space. These introduced fish may carry diseases or parasites which kill resident fish. The new fish may even change the environment, as was the case with the carp, first introduced in Manitoba in 1938. The carp stirs up sediment with its rooting behavior. The change in water clarity is enough to drive away certain species like trout. The fish may be introduced deliberately or by accidental transfer of fish as live bait.

Aquatic plants which spread rapidly and take over large areas can contribute to loss of habitat. Purple loosestrife out-competes many other shoreline and aquatic plants, filling in open water areas and reducing diversity of habitat.