Aquatic invertebrates are essential to wetland function, serving as the key trophic link between primary producers, fish, and waterfowl in boreal wetlands. We studied how both aquatic vegetation complexity and prevalence, and fish presence, could be used to predict the distribution of invertebrate biomass in 24 wetlands of the Western Boreal Forest (WBF). The percent volume occupied by aquatic plants was significantly positively associated with overall invertebrate biomass per liter (P = 0.009). Particular invertebrate functional feeding groups were correlated with types of aquatic macrophyte architecture; herbivorous invertebrate biomass (mg/L) was greater in more complex aquatic environments, and predatory invertebrate biomass was greater in environments with simple plant architecture. Wetlands inhabited by Brook Stickleback (Culaea inconstans) had reduced invertebrate biomass of the predatory, non-predatory (excluding omnivores), and gatherer/collector functional feeding groups. Gatherer/collector, predator, shredder, and piercer invertebrate groups were negatively correlated with dissected leaved plant dominance in those wetlands without fish. These invertebrate groups comprise the bulk of invertebrate protein available to nesting hen mallards and their ducklings. We suggest that the presence of stickleback and/or dominance of dissected leaved plants in the wetlands of the WBF results in decreased food supply for hatchling waterfowl.