We tested the response of several different water quality metrics at 6 sites along a 4-km alternating forest (canopied) and floodplain (non-canopied) reach of the East Branch of the Black River, an undisturbed northern Lower Michigan trout stream, during summer 2015. Physicochemical parameters were unchanged between sites and reflected an undisturbed continuum. In-stream woody debris was higher at the forest sites, whereas relative canopy cover and sunlight intensity were higher at the floodplain sites. Both benthic macroinvertebrates and adult caddisflies exhibited greater species richness and a higher abundance of shredders at the forest sites, and a higher abundance of scrapers at the floodplain sites. Fish specimen abundance, species richness, and percentage of trout were not different between sites, and instead all increased throughout the summer. Community respiration was unchanged between the single tested floodplain site and the forest sites upstream and downstream of it. Gross primary production and net daily metabolism were higher at the floodplain site, leading to stream autotrophy. This result was also obtained when tested in summer 2017. Our results support the idea that terrestrial habitat changes can singularly affect the fundamental ecological functioning of an undisturbed stream, primarily due to deviations in sunlight penetration and allochthonous input. Moreover, the short distances between sites with alternating results indicate the dynamic and serially discontinuous state of natural rivers.