The macroinvertebrate communities of hyporheic and benthic habitats were investigated in relation to stream physicochemistry in glacial, clearwater, and brownwater stream types (n  =  1) during the summer (June–August) of 2004 near Juneau, Alaska. Hyporheic macroinvertebrates were sampled using a series of PVC wells driven into parafluvial bars in the three stream types. Benthic invertebrates were collected using Hess samples from the stream channel adjacent to parafluvial well locations to compare surface macroinvertebrate communities to that of the hyporheic communities. Temperature, total phosphorus, dissolved organic carbon, and total nitrogen concentrations were significantly higher in the brownwater stream compared to the other stream types. Hyporheic macroinvertebrate density was 88% higher in the brownwater stream, despite significantly lower dissolved oxygen concentrations. Benthic macroinvertebrate density was 95% greater in the brownwater stream type than the benthos of the two other stream types. Benthic and hyporheic samples were collector-gatherer driven and the hyporheic zone was functionally more diverse than the benthic habitat with a similar taxa composition across all habitats and stream types. The study of aquatic ecosystems is especially important in Southeast Alaska, where the temperate rainforests are still relatively un-disturbed, and most watersheds still have healthy salmon runs. Our study provides useful data for future management and research in this unique ecoregion, which is predicted to experience substantial climatic changes in temperature and precipitation patterns in the future.