The Eocene Horsefly locality in British Columbia has yielded many fossil fishes, insects, and plants. Its varved sediments make it ideal for study of temporal changes in environment and fish morphology. Several intervals of diatomaceous varves indicate a deep, stratified lake setting. Earlier studies focused on morphological and taphonomic change during the 700-year H2 interval and morphological change during the 10 000-year H3 interval. The present study uses taphonomy as an index for environmental change during the ten millennia represented by H3, comparing taphonomic changes with the morphologic changes found earlier. The H3 interval records deposition in deep water, indicated by dominance of the fish genera Amyzon and Eohiodon. Quiet water conditions are indicated by minimal fin disarticulation. Hypoxia at the time of fish death is confirmed by open mouths of most fish specimens, while cool water on the lake floor prevented full flotation of fish carcasses. Water depth, temperature, and oxygenation fluctuated during H3 deposition. Periods of cooler, deeper, more hypoxic water are indicated by greater numbers and size of Amyzon specimens and by less disarticulation of skull and abdominal bones. Periods of warmer, shallower, more oxygenated waters are indicated by more disarticulation, less fin tetany, smaller fish specimens, and greater diversity of species. Correlations between the taphonomic changes and morphological changes in A. aggregatum are weak. Therefore, the morphological changes are not easily explained as ecophenotypic or short-term evolutionary responses to changes in physical lake conditions.