Biological invasions are a principal threat to global biodiversity. Omnivores, such as crayfish, are among the most important groups of invaders. Their introduction often results in biodiversity loss, particularly of their native counterparts. Managed relocations of native crayfish from areas under threat from invasive crayfish into isolated ‘ark sites’ are sometimes suggested as a conservation strategy for native crayfish; however, such relocations may have unintended detrimental consequences for the recipient ecosystem. Despite this, there have been few attempts to quantify the relative impacts of native and invasive crayfish on aquatic ecosystems. To address this deficiency we conducted a meta-analysis on the effects of native and invasive crayfish on nine ecosystem components: decomposition rate, primary productivity, plant biomass, invertebrate density, biomass and diversity, fish biomass and refuge use, and amphibian larval survival. Native and invasive crayfish significantly reduced invertebrate density and biomass, fish biomass and amphibian survival rate and significantly increased decomposition rates. Invasive crayfish also significantly reduced plant biomass and invertebrate diversity and increased primary productivity. These results show that native and invasive crayfish have wide-ranging impacts on aquatic ecosystems that may be exacerbated for invasive species. Subsequent analysis showed that the impacts of invasive crayfish were significantly greater, in comparison to native crayfish, for decomposition and primary productivity but not invertebrate density, biomass and diversity. Overall, our findings reconfirm the ecosystem altering abilities of both native and invasive crayfish, enforcing the need to carefully regulate managed relocations of native species as well as to develop control programs for invasives.