Environmental gradients strongly influence nearshore lake food webs, altering community assemblages and structuring trophic interactions between taxa. In lake-rich regions, it is common for dissolved organic carbon (DOC) and thermocline depth to vary widely, even amongst nearby lakes. Light attenuation through the water column, a process controlled by these environmental gradients, is an important control on benthic primary production, macroinvertebrate foraging, and nearshore benthic communities. We surveyed nearshore macroinvertebrate communities in 12 lakes in the Adirondack Mountains of New York, where the recovery from historical acid deposition and ongoing warming trends create a natural experiment, to assess community responses to these key environmental gradients. In addition to comparing the taxonomic structure of the assemblage, we evaluate trophic structure using four stable isotope ratios (δ13C, δ15N, δ34S, and δ2H), during two seasons (early stratification and late stratification). We find that warmer, tea-stained lakes supported communities with lower taxonomic diversity with increased prevalence of tolerant taxa. These tannin-rich lakes contained a lower abundance of grazers, higher proportions of predators and collector-gatherers, and were largely lacking sensitive bivalves, amphipods, and plecopterans. We examined patterns of niche differentiation, niche size, and benthic-pelagic coupling across systems and taxa and found that higher DOC concentrations correspond with a contraction in isotopic niche breadth and reduced reliance on benthic resources. These findings suggest that light limitation, which constrains benthic primary production, is not only restricting foraging opportunities for macroinvertebrates but also affecting their taxonomic composition. Decades of acid recovery and climate warming are interacting to increase DOC in Adirondack waters, which is amplifying surface warming rates. Thus, ongoing shifts in surface temperatures and lake color are likely to restructure aquatic food webs by strongly affecting available resources for grazing benthic macroinvertebrates and reducing the clear, oxygenated habitat required by sensitive taxa.