Researchers have recently documented the presence of several groundwater vents in Lake Huron. They are characterized by intruding groundwater that is physico-chemically different from surrounding lakewater which creates benthic gradients of nutrients, dissolved oxygen, and temperature. We studied two vents: (1) a shallow water site in a protected embayment, and (2) an offshore open-water site. We analyzed the distribution and composition of benthic macroinvertebrate and fish communities surrounding the vents and compared them to lake-water control sites. Groundwater sites exhibited differences in the benthic macroinvertebrate community composition relative to control sites, although the shallow groundwater site had higher mean individuals/m² (1527 +/- 702 vs. 513 +/- 276) while the offshore groundwater site had lower individuals/m² (1662 +/- 3117 vs. 4650 +/- 2423) compared to the controls. There were no differences in benthic fish community composition, although groundwater sites had lower CPUE (fish/net-hour) and fish from the offshore site had lower average condition factor. Stable isotope analysis (¹³C, ³⁴S) also shows distinct isotope signatures of the benthic fish and invertebrate communities in the groundwater sites. The data suggest that unique physico-chemical gradients created by the groundwater affect the community composition, distribution, and physiological condition of organisms in the local ecosystems.