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Abstract Some biological invasions can result in algae blooms in the nearshore of clear lakes. We studied if an invasive crayfish (Pacifastacus leniusculus) modified the biomass and community composition of benthic macroinvertebrates and therefore led to a trophic cascade resulting in increased periphyton biomass, elevated littoral primary productivity, and benthic algae bloom in a lake with remarkable transparency [Crater Lake, Oregon, USA]. After quantifying the changes in the spatial distribution of invasive crayfish over a 13-year period, we compared biomass and community composition of littoral–benthic macroinvertebrates, periphyton biovolume, community composition, nutrient limitation, and the development of benthic algae bloom in locations with high and low crayfish density. In addition, we determined if the alteration in community structure resulted in directional changes to gross primary production and ecosystem respiration. The extent of crayfish distribution along the shoreline of Crater Lake doubled over a 13-year period, leaving less than 20% of the shoreline free from crayfish. At high crayfish density sites, benthic macroinvertebrate biomass was 99% lower, and taxa richness was 50% lower than at low crayfish areas. High crayfish sites show tenfold greater periphyton biovolume, sixfold higher periphyton biomass (chlorophylla), twofold higher metabolic productivity, and the presence of large filamentous algae (Cladophorasp.). The invasion of crayfish had negative consequences for a lake protected under the management of the USA National Park Service, with direct impacts on many levels of ecological organization.