Successful plant invasions are hypothesised to be associated with close environmental matching or species poor communities. However, positive correlations between non-native abundance and native plant richness can also arise due to habitat heterogeneity (defined here as variation in abiotic and biotic conditions over space and time). We analysed survey and palaeoecological data for macrophytes in lakes covering a gradient of eutrophication and connectivity to partition the roles of environmental matching, macrophyte diversity and habitat heterogeneity in explaining abundance and invasibility of Elodea canadensis, a widely distributed non-native macrophyte in Europe. There was no association between invasibility and macrophyte species richness. Instead habitat heterogeneity variously enabled the coexistence of native macrophytes and E. canadensis in lake metacommunities over time. Invasion resistance was associated with high native macrophyte cover and unfavourable environmental conditions. We show how spatial and temporal scales can determine the relationship between habitat heterogeneity and invasibility in lake systems.