Wind farms can help to mitigate increasing atmospheric carbon (C) emissions. However, disturbance caused by wind farm development must not have lasting deleterious impacts on landscape C sequestration. To understand the effects of wind farm development on peatlands, we monitored streamwater at Europe’s second largest onshore wind farm (539 MW), Whitelee, Scotland, for 31 months. Using nested catchment sampling to understand impacts on water quality, increasing macronutrient concentrations and exports were associated with wind farm development, particularly forest-felling and borrow pits. Low/poor water quality occurred in small headwater catchments most disturbed by development. At the site exit, dissolved organic C and soluble reactive phosphorus (SRP) concentrations increased during construction, though [SRP] recovery occurred within 2 years. Since C was lost and streamwater quality negatively affected, we propose future good practice measures for wind farm development, including limiting total disturbance within individual catchments and locating borrow pits, where deemed necessary, off site avoiding peatlands.