Stoke Goldington is susceptible to occasional flooding. Some residents in the village suffered badly in 2007. Milton Keynes Council installed measures to reduce the flood risk to the village but unfortunately in May 2018 there was another flood that overcame the new flood defences.

Milton Keynes Council continues to work with Stoke Goldington Parish Council and local residents in relation to, amongst other things, flood defences for the village which includes routine maintenance of drains and ditches.