1. We analysed changes in energy reserves (lipid and glycogen) and length–weight relationships of burrowing mayflies (Hexagenia spp.) in 1997–99 to compare an established population in Lake St Clair with a recovering population in western Lake Erie of the Laurentian Great Lakes. In addition, we measured changes in water temperature and potential food in both water columns and sediments.

2. Although overall mean values of lipid and glycogen levels of Hexagenia nymphs from Lake St Clair and western Lake Erie were not significantly different, there were differences in seasonal patterns between the two lakes. In Lake St Clair, levels were highest in early spring, declined throughout the year, and reached their lowest levels in fall during all 3 years of study. In contrast, levels in western Lake Erie were lower in spring, increased to a maximum in summer, then declined in fall. Seasonal patterns in length–weight relationships were similar to those for lipid and glycogen.

3. Total lipid as a percentage of dry weight did not increase with developmental stage of nymphs until just prior to metamorphosis and emergence from water. However, the major reserve lipid, triacylglycerols, increased systematically with development stage. In the final stage of development, triacylglycerols declined, probably as a result of energy consumption and its conversion to other biochemical components for metamorphosis and reproduction.

4. Indicators of potential food (algal fluorescence in the water column and chlorophyll a and chlorophyll a/phaeophytin ratio in sediments) suggest that Hexagenia in Lake St Clair have a food source that is benthic based, especially in early spring, whereas in western Lake Erie nymphs have a food source that is water column based and settles to the lake bottom during late spring and summer.