Widespread fish introductions have led to a worldwide decline in the number of fishless lakes and their associated communities. Studies assessing effects of fish stocking on native communities in historically fishless lakes have been limited to high-elevation headwater lakes stocked with non-native trout. Little is known about the effect of fish stocking in historically fishless and hydrologically isolated lowland kettle lakes. We compared the effects of introduced fish on macroinvertebrate communities in kettle lakes stocked with centrarchids, salmonids, and cyprinids, and headwater lakes stocked with brook trout (Salvelinus fontinalis) in Maine, USA. Fish had significant effects on macroinvertebrate community structure in both lake types, with reduced species richness and abundances of taxa characteristic of fishless lakes. The effects of introduced fish were more pronounced in headwater lakes despite a less diverse fish assemblage than in kettle lakes. We attribute this to abundant submerged vegetation providing refuge from fish predation and reduced stocking frequency in kettle lakes. We assessed effects of stocking duration on macroinvertebrates in a subset of headwater lakes with known dates of trout introduction. Species richness and abundance of most taxa declined within 3 years following trout introduction; however, richness and abundance were least in lakes with long stocking histories (≥40 years). Macroinvertebrates previously identified as fishless bioindicators were absent from all stocked lakes, indicating that trout rapidly eliminate these sensitive taxa. Conservation of this historically undervalued ecosystem requires protecting remaining fishless lakes and recovering those that have been stocked.