Coldwater trout streams are important natural resources in northeast Iowa. Extensive efforts have been made by state and federal agencies to protect and improve water quality in northeast Iowa streams that include Sny Magill Creek and Bloody Run Creek, which are located in Clayton County. A series of three water quality projects were implemented in Sny Magill Creek watershed during 1988 to 1999, which were supported by multiple agencies and focused on best management practice (BMP) adoption. Water quality monitoring was performed during 1992 to 2001 to assess the impact of these installed BMPs in the Sny Magill Creek watershed using a paired watershed approach, where the Bloody Run Creek watershed served as the control. Conservation practice adoption still occurred in the Bloody Run Creek watershed during the 10-year monitoring project and accelerated after the project ended, when a multiagency supported water quality project was implemented during 2002 to 2007. Statistical analysis of the paired watershed results using a pre/post model indicated that discharge increased 8% in Sny Magill Creek watershed relative to the Bloody Run Creek watershed, turbidity declined 41%, total suspended sediment declined 7%, and NOx-N (nitrate-nitrogen plus nitrite-nitrogen) increased 15%. Similar results were obtained with a gradual change statistical model.The weak sediment reductions and increased NOx-N levels were both unexpected and indicate that dynamics between adopted BMPs and stream systems need to be better understood. Fish surveys indicate that conditions for supporting trout fisheries have improved in both streams. Important lessons to be taken from the overall study include (1) committed project coordinators, agency collaborators, and landowners/producers are all needed for successful water quality projects; (2) smaller watershed areas should be used in paired studies; (3) reductions in stream discharge may be required in these systems in order for significant sediment load decreases to occur; (4) long-term monitoring on the order of decades can be required to detect meaningful changes in water quality in response to BMP implementation; and (5) all consequences of specific BMPs need to be considered when considering strategies for watershed protection.