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The escalating spread of invasive species increases the risk of disrupting the pathways of energy flow through native ecosystems, modify the relative importance of resource ('bottom-up') and consumer ('top-down') control in food webs and thereby govern biomass production at different trophic levels. The current lack of understanding of interaction cascades triggered by non-indigenous species underscores the need for more basic exploratory research to assess the degree to which novel species regulate bottom-up and/or top down control. Novel predators are expected to produce the strongest effects by decimating consumers, and leading to the blooms of primary producers. Here we show how the arrival of the invasive crab Rhithropanopeus harrisii into the Baltic Sea - a bottom-up controlled ecosystem where no equivalent predators ever existed - appeared to trigger not only strong top-down control resulting in a decline in richness and biomass of benthic invertebrates, but also an increase in pelagic nutrients and phytoplankton biomass. Thus, the addition of a novel interaction - crab predation - to an ecosystem has a potential to reduce the relative importance of bottom-up regulation, relax benthic-pelagic coupling and reallocate large amounts of nutrients from benthic to pelagic processes, resulting in a regime shift to a degraded ecosystem state.