The term "invertebrate" covers a vast number of animal species, anything from single-celled creatures to jellyfish to spiders to lobsters. Like elsewhere in the world, invertebrates make up more than three quarters of the species of animals in Cape Breton.

Invertebrates can be herbivores, keeping plants and trees in check. They can be carnivores, eating other invertebrates as well as larger animals. They can be parasites, keeping the numbers of a certain type of plant or animal down, and perhaps most important of all, they can be detritivores, eating dead animal and plant matter and in doing so, releasing important nutrients back into the environment so they can be used by other plants and animals. Most invertebrates are food for other species of animals and even for carnivorous plants like the sundew.

Land-based and freshwater invertebrates

More than 4,000 species of land-based and freshwater insects and spiders have been identified within Cape Breton Highlands National Park.

Stoneflies and caddisflies, which live in freshwater streams and ponds, are important sources of food for trout and salmon. Bees and wasps are important for pollination of plants. Dragonflies eat other insects. Many species of beetle are detritivores. The spruce budworm helps keep the boreal forest from becoming a monoculture stand of balsam fir, which would decrease biodiversity.

Terrestrial snails and slugs are also invertebrates. Other molluscs such as freshwater mussels, clams and snails are part of the food chain in the park's rivers and lakes. One species of special interest is the valve snail, which lives in Freshwater Lake. This is the only known site for this animal in Nova Scotia.

Introduced invertebrates include earwigs, earthworms and several forest insects.

Intertidal Invertebrates

Cape Breton Highlands National Park does not have a lot of intertidal invertebrates because of small daily tidal changes and because the coast is unprotected and frequently pounded by waves and scoured by ice.

Invertebrates that may be found on rocky headlands in the park include sea stars, the green sea urchin, rock crab, blue mussel, periwinkle, dog whelks and barnacles. The few sand beaches in the park provide habitat for sand dollars, moon snails, clams and a variety of amphipods such as the beach flea. Cobble beaches are common in the park but provide very little habitat for invertebrates because of the constant tumbling of the cobbles by the waves.

Introduced intertidal invertebrates include isopods and the green crab, which is a potential threat to mussel populations.

Marine Invertebrates

The most well-known and commercially important marine invertebrates are lobster and snow crab. Other marine invertebrates which are important from an ecological point of view are zooplankton species (tiny shrimp and other animals). These small creatures make up the bulk of the diet of the plankton-eating basking shark and many other fish and of baleen whales like the humpback and fin whale. Jellyfish are also commonly found in the waters off Nova Scotia and are the main diet of the endangered leatherback turtle.