The global spread of invasive species is changing the structure of aquatic food webs worldwide. The North American Great Lakes have proved particularly vulnerable to this threat. In nearshore areas, invasive benthic species such as dreissenid mussels and round gobies (Neogobius melanostomus) have gained dominance in recent years. Such species are driving the flow of energy and material from the water column to the benthic zone, with dramatic effect on nutrient and contaminant cycling. Here, we develop a stage-structured model of a benthified food web in Lake Michigan with seasonal resolution and show how its bioaccumulation patterns differ from expected ones. Our model suggests that contaminant recycling through the consumption of lipid-rich fish eggs and mussel detritus is responsible for these differences. In southern Lake Michigan's Calumet Harbor (Chicago, IL, USA), round gobies have nitrogen isotope signatures with considerable spread, with some values higher than their predators and others lower than their prey. Contrary to patterns observed in linear pelagic systems, we predict that polychlorinated biphenyl (PCB) concentrations in these fish decrease with increasing size due to the lipid- and benthos-enriched diets of smaller fish. We also present here round goby PCB concentrations measured in 2005 after an invasional succession in Calumet Harbor and demonstrate how the change from one invasive mussel species to another may have led to a decrease in round goby PCB accumulation. Our results suggest that benthic-dominated systems differ from pelagic ones chiefly due to the influence of detritus and that these effects are exacerbated in systems with low species diversity and high biomass.