We examined long-term ecological change in two Hudson River tributaries, the Wappinger and Fishkill Creek watersheds in Dutchess County, New York State. Fish data spanning 65\ years (1936, 1988, 1992, and 2001) and shorter term macroinvertebrate data (1988, 2001) were used to assess the influence of land use practices. Between 1988 and 2001, macroinvertebrate index Biotic Assessment Profile (BAP) improved by 113–165\% in the Fishkill Creek watershed, and fish Index of Biotic Integrity (IBI) improved by 117–140\%. Fish IBI and fish species richness were significantly different (p \< 0.01) between the watersheds, with Wappinger Creek in better condition. Long-term fish IBI scores showed degradation in both watersheds since the 1930s. Changes in species composition suggest community homogenization on par with overall changes in the fish fauna of New York. Most notable were increases in tolerant species and declines in intolerant or moderately tolerant species. Whereas Fishkill Creek IBIs showed decline in 1988 relative to 1936, followed by improvement, Wappinger Creek declined monotonically in environmental quality. Development has intensified in both watersheds, but Fishkill Creek is improving while Wappinger Creek watershed is undergoing less mitigated degradation. We find that older, semi-quantitative data can be used to construct environmental quality indicators, and can be of great use for measuring long-term change.