There are some great resources for paddling the Great Ouse.
Go Paddling offers a one-stop-shop for where to paddle and useful tips from other paddlers. They also offer guides for paddling the principle fenland drains: The Old Bedford River and New Bedford River
The River Obstacles Database is a definitive resource for things that will get in your way.
If you are looking to hire a canoe in the Milton Keynes area, then Canoe the Ouse is worth contacting.
For Bedford, try Canoe Trail.
The National Trust have prodiced some guidance on canoeing from Houghton Mill: Canoeing from Houghton Mill