Preservation of biodiversity depends on restoring the full range of historic environmental variation to which organisms have evolved, including natural disturbances. Lotic ecosystems have been fragmented by dams causing a reduction in natural levels of environmental variation (flow and temperature) and consequently a reduction of biodiversity in downstream communities. We conducted a long-term study of the macroinvertebrate communities before and after natural flood disturbances in an unregulated reference site (natural flows and temperatures), a regulated site (regulated flows and temperatures), and a partially regulated reference site (regulated flows and natural temperatures) on the upper Colorado River downstream from a deep-release storage reservoir. We aimed to test the hypothesis that floods and temperature restoration would cause an increase in macroinvertebrate diversity at the regulated site. Over the short term, macroinvertebrate richness decreased at the regulated site when compared to pre-flood levels, whereas total macroinvertebrate density remained unchanged. Over the long term (1 and 10 years after the floods), macroinvertebrate diversity and community structure at the regulated site returned to pre-flood levels without increasing to reference conditions. Occasional floods did not restore biodiversity in this system. As long as the physical state variables remain altered beyond a threshold, the community will return to its altered regulated condition. However, temperature restoration at the partially regulated site resulted in an increase in macroinvertebrate diversity. Our results indicate that restoration of the natural temperature regime will have a stronger effect on restoring biodiversity than occasional channel-forming floods.