Many Great Lakes fish species use wetlands for feeding, cover, spawning, and nursery habitat. Some fish stay in marshes for most of the year, but seasonal visits are more common.
Those fish that spawn in the early spring after the ice melts leave immediately after depositing their eggs. These fish, which include Northern Pike, take advantage of the warm shallow water temperatures and high dissolved oxygen levels in the water, which is required for egg respiration.
Other fish spawn in late spring to early summer, and the male stays with the eggs, fanning them to provide the needed oxygen, and guard the eggs from predators. An example of these fish includes the Largemouth Bass.
Second Marsh once sustained large populations of game fish such as Northern Pike and Smallmouth Bass. Due in part to water level changes and an increase in sediment loading, these species have been much reduced in numbers. Steps are being taken under the new Management Plan to rectify this.  The Common Carp is present in Second Marsh. This species has greatly increased in numbers and is becoming destructive, by disturbing sediments and destroying the vegetation. The marsh restoration project is designed to create a more balanced fish population and manage nuisance plant species.
The official list of species in Ontario according to the Ontario Ministry of Natural Resources (Oct. 1997) stands at 158 species.  Of these, 57 species have been recorded for the Second Marsh, Harmony, Farewell and Black Creeks and the immediate offshore waters.
American Brook Lamprey
Sea Lamprey
American Eel
Gizzard Shad
Common Carp
Brassy Minnow
Common Shiner
Golden Shiner
Emerald Shiner
Blacknose Shiner
Spottail Shiner
Rosyface Shiner
Sand Shiner
Pearl Dace
Northern Redbelly Dace
Finescale Dace
Bluntnose Minnow
Fathead Minnow
Blacknose Dace
Longnose Dace
Creek Chub
Longnose Sucker
White Sucker
Brown Bullhead
Channel Catfish
Tadpole Madtom
Northern Pike
Central Mudminnow
Rainbow Smelt
Coho Salmon
Rainbow Trout
Chinook Salmon
Brown Trout
Brook Trout
Banded Killifish
Brook Stickleback
Mottled Sculpin
Slimy Sculpin
White Perch
White Bass
Rock Bass
Smallmouth Bass
Largemouth Bass
Black Crappie
Rainbow Darter
Iowa Darter
Least Darter
Johnny Darter
Yellow Perch