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 as well as buying membership which covers permits and insurance.
They also offer guides for paddling the principle fenland drains:
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