In my microscopic analysis of my aquariums. My axolotl's tank has numerous planktonic just-visible-to-the-eye (0.1-2 mm?) organisms swimming around in there, while my mudpuppy's tank has very few of these. I only got lucky once to capture a dead one once and see it under the scope, clearly it was some ugly crustacean, but since it was dead, I don't know if it was specifically a Daphnia.
The main difference between the tanks is lighting. Mudpuppy has a run of the mill pet store chain light apparatus/bulb. On the axolotl's tank I purchased the light at a local aquarium shop that specializes in planted tanks and is ridiculously bright to penetrate the water.
Looking at the microrganisms that the plankton feed on, the tanks correlate well. My axolotl and mudpuppy's tank have the same diversity of organisms, (ameoba, algae (desmids, diatoms, etc), cilliates, nematodes, rotifers...) but the numbers present in the well lit aquarium are astounding.
Also in terms of transferring pond water. You always have to be cautious, since you don't know what you're going to get with that water. However, Looking at objects in the tank. Simple water seems to be relatively sparsely populated, while the surfaces of stones and logs are much richer. So you may get more bang for your buck if you move objects over water from the pond.
I never had cloud minnows, but I suspect these are going to work against your desire. Fish tend to eat everything they can in my hands.
In summary, I think lighting may be key if you want to establish your pond set up. Also you can read how people culture daphnia and try to work some of their tricks into your tank. But I think if you can get a rich plant life established in an aquarium, you'll have the right environment.