Interesting post. I am off to investigate some of the plants that were mentioned. Thanks.

Vickster, your lilies should be okay left on the shelf, if they are too heavy and awkward to sink to the bottom of your pond. As long as they are not tropicals and the water covers them all winter they will survive. I winter hardy lilies,without a problem, stored in a kiddie pool that is only 9" deep and it freezes solid. As for the rest of your questions, checkout the link below to another post on this forum similar to yours. "Horton" Here is a link that might be useful: Winterising information

Actually, a fair number of commercially available pond plants are natives: lizardtail (Saururus cernuus) fragrant water lily (Nymphaea odorata) blue flag iris (Iris versicolor) cardinal flower (Lobelia cardinalis) giant blue lobelia (Lobelia siphilitica) buckbean (Menyanthes trifoliata) golden club (Orontium aquaticum) arrow arum (Peltandra virginica) arrowhead (Sagittaria latifolia, etc) marsh marigold (Caltha palustris) threeway sedge (Dulichium arundinaceum) cottongrass (Eriophorum) common rush (Juncus effusus) cattails (Typha latifolia, Typha angustifolia, but note that some other Typha species are not native) thalia (Thalia dealbata) -- not native to Maryland, but native elsewhere in the south dwarf horsetail (Equisetum scirpoides) -- native farther north creeping spearwort (Ranunculus flammula) -- native farther north

What above poster said - that space is nowhere near large enough for koi, which get 2-3 feet long. They require about 4-5 feet depth + minimum 1000 gals per fish. Sarassa comets (ie type of goldfish) are better choice and can get very koi-like with long flowing fins - however Im not sure its deep enough for even comets. If not red minnows are great for small ponds. I would start by clearing out muck and decaying organic debris - if you dont have a compost pile now would be a good time to start one! First see what you have - how deep, how do the 2 parts connect, are they same level or does one meant to flow into the other? Is the liner still any good? I wonder if it was designed to be a pond or a water garden?. Identify what the established plants are - looks like there may be some iris? - and which you will want to keep. Or a bog - bottom photo looks like a bog. Perhaps water flowed through there (if it was intended to be a bog) and then flowed down to the other section? Or perhaps it was neglected so long that the plants started growing in the debris. In any event I think I would just start by seeing what exactly you have and then posting that, along with your ideas of what you would want it to be, on the pond forum. Yeah, not sure why this forum is here - no expert koi keepers posting that I can tell. I just stop by occasionally - 9 times out of ten its just letting people know their ponds are too small for koi LOL. EDITTED TO ADD - first step before cleaning out muck -identify the live established plants bc you may want to be keeping those and maybe all it needs is the leaves cleaned out (somewhat) and the pond to be refilled if its to be a more naturalistic pond.