The Atlantic Forest of southeastern Brazil is famous for its richness, endemism, and its status as one of the most threatened ecosystems on earth.  Much of the remaining forest is fragmented within an agriculturally-dominated landscape.  Little is known about the status of stream communities in these forest fragments or in adjacent deforested regions.  The long-term effects of links between forest fragment and agricultural matrix streams are also poorly understood.  To address these questions, we compared longitudinal trends of fish communities in third-order streams of a 2000ha Atlantic forest fragment with those of adjacent agricultural lands that were deforested in the 1920s.  Although 16 of 23 species documented were common to the forest fragment and the agricultural matrix, longitudinal trends differed.  Ordinations showed that fish communities of the agricultural matrix had shifted in an upstream direction, mixing disturbance-tolerant species with those more typical of headwaters.  In forest streams, disturbance-tolerant species were largely restricted to recently aggraded channels at the downstream edges of the fragment.  In contrast, another species was found only in the core of the forest fragment.  This species and its habitat may be threatened by further channel aggradation and upstream encroachment of disturbance-tolerant fishes.