Read and re-read Ewests post above. You cannot effectively submit a proposal and budget until you have an idea what the client actually wants and equally important whether or not what the client wants is feasible and/or a reasonable expectation.
Being a consultant also means knowing which projects you need to walk away from. You can't be everything to everyone.
As a consultant you will "give away" quite a bit of knowledge for free. I "give away" advice all of the time (some of it is even good advice

). Get use to it. You must demonstrate to the client that you have vast knowledge related to this subject and that is why they need to hire you. IMHO you need to use the proposal to showcase how much you know. Discuss the effect of the uncertain elements that you mentioned above (surface area, depth, fertility, etc).
As a consultant you will write numerous proposals. Many will be rejected. Leave your ego at the door.
That's excellent advice. Unfortunately there's a lot more to contract work besides doing a good job. You or someone in the organization has to sell it to the client before you even get a chance.
Before doing anything you must have a defined scope of your role from the potential client. In the realm of Project Management in the Construction and Engineering sector there must be an open dialogue between contractor and client. Also bid packages are put together by prospective clients to outline their needs.
It is within reasonable expectation that the client goes through a high level scope of the project and their goals before any quotations. At this time you should ask for any other details that you deem pertinent to executing your piece of the puzzle.
Your quote must be concise and have a detailed breakdown of line items. Outline each portion of your services (Fish, Plants, Feed, Structure, etc.). This is your chance to put a price tag on each stage of your contract. As JHAP says this is where you are giving information away for free. However if done correctly you can paint broad strokes(Fish: Main line Predators"$2500", Omnivorous Forage Fish"$1500", Feeder minnows "$500").
I realize that Fisheries Consulting is different animal from the Engineering world, but IMO a quote serves the purpose of outlining the steps and prices needed to achieve the client's objective. It shows what is included, but more importantly what isn't. If the quote is accepted then you and the client have agreed to pricing and scope of your work. When the scope changes (It always does) you are not obligated to do that work. Anything else can be paid for in "Time & Materials".
Good luck and be careful. Something seems off here IMHO. You should know what they want before any quotes are delivered. I hope this helps...