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ABSTRACT Ecosystems are abruptly changing due to invasive species and global climate change. In lakes, invasive Rainbow Smelt Osmerus mordax can cause negative ecosystem effects through competitive and predatory interactions with native species leading to food web shifts away from native species dominance, altered zooplankton communities, and the decline or extirpation of native cool and coldwater fishes. We conducted two whole-lake removals of invasive Rainbow Smelt and simultaneous introductions of native Cisco Coregonus artedi through stocking. About 327 and 1.6 adult Rainbow Smelt/ha were removed and about 45 adult Cisco/ha were stocked over 4 years into the two experimental lakes. In one system, native Yellow Perch Perca flavscens relative abundance and density significantly increased by 556% and 143% post-manipulation, respectively. In the other system, native Walleye Sander vitreus relative abundance increased by 26% and became consistently present in the pelagic zone post-manipulation (allowing for density estimation). Rainbow Smelt relative abundance and density decreased by >85% in both experimental lakes. The two ecosystems shifted to native species dominance while invasive Rainbow Smelt became insignificant components of the food webs. In these two intensive whole-lake manipulations, we applied the Resist–Accept–Direct (RAD) climate adaptation framework to test an applicable ecological adaptation strategy and used panarchy theory as an ecologically grounded pathway to purposefully direct ecosystem transformation. We used this holistic management framework to better understand and manage undesired ecological change—“food web thinking.” In the context of our study, two ecosystems were purposefully directed towards native food web structures, species interactions, and processes, which mitigated Rainbow Smelt driven negative effects.