Mounting evidence suggests that fishing can trigger trophic cascades and alter food web dynamics, yet its effects on ecosystem function remain largely unknown. We used the large-scale experimental framework of four marine reserves, spanning an oceanographic gradient in northeastern New Zealand, to test the extent to which the exploitation of reef predators can alter kelp carbon flux and secondary production. We provide evidence that the reduction of predatory snapper (Pagrus auratus) and lobster (Jasus edwardsii) can lead to an increase in sea urchins (Evechinus chloroticus) and indirect declines in kelp biomass in some locations but not others. Stable carbon isotope ratios (delta13C) of oysters (Crassostrea gigas) and mussels (Perna canaliculus) transplanted in reserve and fished sites within four locations revealed that fishing indirectly reduced the proportion of kelp-derived organic carbon assimilated by filter feeders in two locations where densities of actively grazing sea urchins were 23.7 and 8.3 times higher and kelp biomass was an order of magnitude lower than in non-fished reserve sites. In contrast, in the two locations where fishing had no effect on urchin density or kelp biomass, we detected no effect of fishing on the carbon signature of filter feeders. We show that the effects of fishing on nearshore trophic structure and carbon flux are context-dependent and hinge on large-scale, regional oceanographic factors. Where cascading effects of fishing on kelp biomass were documented, enhanced assimilation of kelp carbon did not result in the magnification of secondary production. Instead, a strong regional gradient in filter feeder growth emerged, best predicted by chlorophyll a. Estimates of kelp contribution to the diet of transplanted consumers averaged 56.9% +/- 6.2% (mean +/- SE) for mussels and 33.8% +/- 7.3% for oysters, suggesting that organic carbon fixed by kelp is an important food source fueling northeastern New Zealand's nearshore food webs. The importance of predators in mediating benthic primary production and organic carbon flux suggests that overfishing can have profound consequences on ecosystem functioning particularly where pelagic primary production is limiting. Our results underscore the broader ecosystem repercussions of overfishing and its context-dependent effects.