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Timber harvest temporarily increases water yield; however, relationships between hydrologic and nutrient chemistry changes have not been consistent. This study quantified the effects of forest harvesting and site preparation without fertilization and with modern best management practices on nutrient concentrations and yields in small headwater streams of the Southeastern Coastal Plain. We monitored two watershed pairs for 2 years prior to and 1 year following timber harvest and for 2 more years following site preparation and planting. Treatment watersheds were clearcut, and downstream portions of streamside management zones were thinned in Fall 2003. Site preparation (herbicide application and burning) and planting followed a year later. All operations followed 1999 Georgia forestry best management practices. Previously published research revealed a large increase in water yield following harvest. Nutrient concentrations varied significantly within and between monitoring periods, even in reference watersheds. Silvicultural activities had no discernible effect on phosphorus and ammonium concentrations; however, statistically significant increases in nitrate/nitrite (67–340 μg L−1) and total nitrogen concentrations (100–400 μg L−1) in treatment watersheds followed stand re-establishment. Nutrient yields increased after timber harvest largely as a result of increased water yields, although increased nutrient yields were small relative to inter-annual and inter-watershed variability and variability. Annual water yield largely explained the variability in annual nitrogen and phosphorus export from reference and treatment streams (r2 values from 0.65 to 0.98). High NOx concentrations coming from an upstream agricultural area decreased 1600–1800 μg L−1 over several hundred metres in the treatment streams by dilution, uptake or denitrification. Copyright © 2013 John Wiley & Sons, Ltd.