Implementation of best management practices (BMPs), such as improved manure storage, buffer strips, and grassed waterways, through government funded conservation programs is a common approach for mitigation of the impacts agricultural activities have on the surrounding environment. In this study, we tested the ability of these practices to meet the environmental goal of improved stream quality at a “micro-basin” scale in the Upper Thames River Watershed, southern Ontario, Canada. Micro-basins were first and second order basins, averaging 400 ha in area, representing gradients of land cover, geomorphology, and participation in conservation programs. At the outflow of each micro-basin the benthic macro-invertebrate community was sampled, water chemistry measurements completed, and habitat quality assessed. Results showed micro-basins with relatively high levels of BMP implementation consistently demonstrated improved stream ecosystem quality over the majority of micro-basins with low or no implementation. Streams in the Upper Thames River basin appeared to exhibit a threshold effect, where with several BMPs in the same basin an improvement in stream ecosystem quality is visible. In addition to the BMPs implemented through government funded conservation programs, the observed ecosystem improvements are probably due to increased environmental awareness and improved management by farmers.