Fishless lakes, which may harbour higher biodiversity than lakes with fish, are becoming increasingly rare due to fish introductions. Although the impacts of fish introduction are relatively well studied in high-elevation fishless lakes, previous studies have mainly focused on a single invertebrate community or on a particular life stage of a given organism, such as amphibians. In this study, we examined how zooplankton and amphibian communities differ between fishless and fish-bearing kettle lakes, allowing us to determine whether fish presence affects these communities and how this happens by identifying the species and life stages affected. Furthermore, some kettle lakes are hydrologically connected to surrounding aquatic ecosystems, which allows natural colonization by fish. We therefore also evaluated how amphibian and zooplankton communities differ between connected and disconnected kettle lakes. By comparing 36 kettle lakes in Québec, Canada, we found that fish presence was associated with differences in species abundance at each stage of the amphibian life cycle. Reproductive calls of adult amphibians were detected regardless of fish presence, indicating that reproduction occurred in all lake types. However, the presence of fish was associated with fewer amphibian egg masses and lower larval abundance, and the absence of salamanders at the larval stage. Small-bodied zooplankton were more abundant in fish-bearing lakes, while overall species richness was lower. In particular, Chaoborus americanus, a large predatory zooplankton species, was found exclusively in fishless lakes. While hydrological connectivity had no significant effect on most communities, it did influence the abundance of adult American toads, adult wood frogs, and mink frogs' tadpoles, which responded positively to the interaction between fish presence and connectivity. We recommend avoiding fish stocking of kettle lakes to preserve essential reproductive habitats for amphibians, maintain refuges for sensitive zooplankton species, and safeguard the spatial heterogeneity that underpins landscape-scale biodiversity.