I'm going to add my situation and possible solution to this thread since it's similar.

I "finished" my pond at the beginning of spring. Just in time for some nice rain. Started to fill quickly, then July happened. Little to no rain and my water line is going down. It's about a 1/3 full at the moment with a few species of fish already introduced.

This pond sits right next to, but uphill from, a creek that flows year round. It is quite the trek uphill to the pond's bank, but they basically share the same shoreline.

I had completely ruled out the option of filling from the creek early on, especially when sampling said creek and realizing that I could possibly introduce some nearly microscopic species. And I'd have no clue what they were. But this low water and no rain has me nervous and I want it to fill badly. So I'm considering it again, but with some conditions.

There is no electricity at the pond and I don't live on it. So even a trash pump wouldn't work. I was considering a hydraulic ram, however, there's not a lot of elevation with this creek. It's all pretty level. I'm going to do some looking around this weekend to see if there's a spot where I can make this work.

Here's the crux of the plan, an idea given to me by a friend of mine who many of you met at PBV, Alex. The water coming from the creek, uphill, enters a 55 gallon plastic drum before entering the pond. This drum is filled halfway, or 2/3 of the way, with sand and gravel. Holes are drilled into the bottom of the drum to allow this water to enter the pond, which, in theory and in hopes, would be now free of unwanted species from the creek.

Pond is approximately one acre. Species will be redear sunfish, yellow perch, smallmouth bass, wipers and walleye.

Below is a diagram (oldish aerial photo) of where the pond (outlined in red) is in relation to the creek (blue line).