Shallow high-latitude lakes and ponds are usually characterized by an oligotrophic water column overlying a biomass-rich, highly productive benthos. Their pelagic food webs often contain abundant zooplankton but the importance of benthic organic carbon versus seston as their food sources has been little explored. Our objectives were to measure the δ13C and δ15N isotopic signatures of pelagic and benthic particulate organic matter (POM) in shallow water bodies in northern Canada and to determine the relative transfer of this material to zooplankton and other aquatic invertebrates. Fluorescence analysis of colored dissolved organic matter (CDOM) indicated a relatively strong terrestrial carbon influence in five subarctic waterbodies whereas the CDOM in five arctic water columns contained mostly organic carbon of autochthonous origin. The isotopic signatures of planktonic POM and cohesive benthic microbial mats were distinctly different at all study sites, while non-cohesive microbial mats often overlapped in their δ13C signals with the planktonic POM. Zooplankton isotopic signatures indicated a potential trophic link with different fractions of planktonic POM and the non-cohesive mats whereas the cohesive mats did not appear to be used as a major carbon source. The zooplankton signals differed among species, indicating selective use of resources and niche partitioning. Most zooplankton had δ13C values that were intermediate between the values of putative food sources and that likely reflected selective feeding on components of the pelagic or benthic POM. The results emphasize the likely importance of benthic-pelagic coupling in tundra ecosystems, including for species that are traditionally considered pelagic and previously thought to be dependent only on phytoplankton as their food source.