Drainage water management such as controlled tile drainage (CTD) is one means to help meet pollution mitigation targets and boost crop yields. In this study, CTD was retrofit to existing tile drained fields in eastern Ontario, Canada (humid continental climate) to study water quality benefits. A suite of paired field systems were used to compare CTD tile drainage quality with conventional tile drainage quality for nine growing seasons (2005–2013), translating to 35 field-crop years. Field crops were corn, soybean and forage. For CTD fields, controlled tile drainage was employed only during the growing season (time period when comparisons were made) due to surface runoff/erosion and growing season length concerns associated with non-growing season flow control. Water quality targets in tile effluent included: nitrate, ammonium, total phosphorus, dissolved reactive phosphorus, and fecal indicator bacteria such as E. coli, and Enterococci. Respectively, there were 60, 51, 58, 66, 66, 76, and 25% reductions in above noted drainage water fluxes and water quality targets as a result of CTD (for all 35 field-crop years combined). Concurrent environmental and potential public health benefits of managing tile drainage during the growing season were demonstrated; moreover, over the course of the study, corn and soybean yields were significantly boosted by CTD.