Stream acidification across the northeastern US impacts fish abundance and fish communities. In this study, we document a fish community shift in the upper mainstem of Hubbard Brook (NH) from the presence of at least three species in the 1960s to the presence of only one species today. Cottus cognatus (Slimy Sculpin) and Rhinichthys atratulus (Blacknose Dace) are no longer present in this system, and we suggest that extirpation occurred during a period of chronic acidification during the early 1970s. Today, Salvelinus fontinalis (Brook Trout) is the only fish species present in the upper reaches of the Hubbard Brook Valley. The current upstream extent of Brook Trout is limited primarily by physical obstructions such as waterfalls or cascades. Acidification may lead to chemical barriers that limit upstream movement during high flow in a few streams. As recovery from acid deposition begins, and as regional climate changes, our observations demonstrate the value of periodic evaluations documenting shifts in the distribution and composition of fish communities in headwaters of the northeastern US.