That's not small.
Do you have a hydrologist working on this? You need an engineer that knows his stuff regarding hydrology and hydraulics so you know what sorts of volumes and flow rates to deal with. If that's you, that's cool, I'm just saying. Sometimes folks show up on these forums hoping for a simple answer to a complex problem. If you don't have a hydrologist yet, get one.
We still don't really know enough about this thing to answer the question though. An acre pond in Jersey with a "liner that needs maintenance" sounds like a concrete lined pond, yes? And it was for what, flood control? Any other (water quality?) functions to it? And it handles how big of a drainage area of what nature? Does it handle pollutants or industrial runoff or anything weird? Who's your client?
What sort of 'liner' does it need exactly, and is there anything preventing you from going with a textile solution, stitching the whole thing together nearby, and just rolling it out into the pond on a dry day?
My first impression, presuming we're talking about an acre concrete box and some sort of liner coating that requires curing time: Can you throw up a wall down the middle and work on one half while the other half is active?
Hydrology, Drainage Analysis, Flood Studies, and Complex Stormwater Litigation for Atlanta and the South East -