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According to apparent competition theory, sharing a predator should cause indirect interactions among prey that can affect the structure and the dynamics of natural communities.Though shifts in prey dominance and predator resource use along environmental gradients are rather common, empirical evidence on the role of indirect prey–prey interactions through shared predation particularly with increasing productivity, is still scarce.In an 8‐week lake mesocosm experiment, we manipulated both the addition of inorganic nutrients and the presence of generalist fish predators (crucian carp, Carassius carassius L.), to test for the effects of indirect interactions through shared predation along a productivity gradient.We found that apparent mutualism (indirect positive interaction) between benthic and pelagic prey strongly affected short‐term responses of aquatic food webs to increasing productivity in the presence of a generalist fish. Increasing productivity favoured the relative abundance of benthic prey, following trends in natural productive lake systems. This led to a shift in fish selectivity from pelagic to benthic prey driven by changes in fish behaviour, which resulted in apparent mutualism due to the lower and delayed top‐down control of pelagic prey at increasing productivity.Our results show empirical evidence that the coupling of multiple production pathways can lead to strong indirect interactions through shared predation, whereby prey dynamics on short time‐scales are highly dependent on the foraging behaviour of generalist predators. This mechanism may play an important role in short‐term responses of food webs across environmental gradients., In an aquatic mesocosm study, the authors found that switching foraging in a generalist predator can lead to short‐term apparent mutualism between its benthic and pelagic prey. Such indirect prey–prey interactions had important consequences in prey community dynamics and strongly affected the food web response to increasing productivity.