The USDA Natural Resource Conservation Service has many local offices that can assist with designing and even obtaining grants for projects like this. This agency is helpful and does not play any regulatory role. You should feel free to consult with them. They may even vist your property to provide onsite assistance and advice.
You are not going to like this, but almost any modifcation of a creek bank such as digging, crossings, retaining wall gabions, daming or filling, is highly regulated. Many of these activities require a Section 404 permit from the Army COE. The idea is to protect water quality and mitigate damage from alterning the natural course of streams. This is a classic case of where your land has come under the regulatory perview of certain Federal Agencies. Although there are some grant funds to help landowners with the financial burdens of managing streams and meeting regulatory restrictions, these funds are rare. More often modifications done outside of the regulatory framework and oversight are potenially subject to huge fines and costs of restoration.
Minor activities are often exempt from these regulations, but you need to become aware of at what point your project goes from minor to regulated. Stream work can be divided into three categories: minor activities which do not require a permit, activities which are authorized by existing state guidance, and activities which need to be authorized by an individual permit. Contrary to popular belief, most permit applications for stream work are approved. In most places you can plant trees or vegetation to prevent erosion. You may also stabilize up to 200 feet of streambank with non-erodable materials. The above being just a word to the wise.
The advise is to consult with the NRCS in your area so that whatever you do does not put you in the gunsights of the regulatory agencies that manage discharge permits and the Corps of Engineers. If you need a permit, get it! The processing fees are as low as $50 but penaties and costs for doing regulated work outside of a permit can cost you everything you own.
Please post back with any questions. If you indicate what State you are in, I may be able to direct you to some appropriate resources.