Some of the quarry ponds in my area have very little aquatic plant growth around the shoreline - which is atypical compared to the more conventional ponds frequently discussed on the forum.

Is your shore mostly steep rock sides dropping nearly vertically into deep water?

If so, then nearly all of the "fertility" of your pond is available ONLY to suspended organisms.

Do you have a shallow end with some decent substrate? One option would be to plant some desired aquatic plants. Hopefully, that would take up some of the fertility available to the photosynthesizing algae, yet not impede the food chain for the zooplankton. If the rest of the pond is a relatively hostile environment to rooted aquatic plants, then you could even plant some of the slightly more aggressive "spreading" species.

Another option is some floating islands of plants. I have seen quarries with visibility down to 30'. Maybe some floating islands would take up some plant nutrients and provide a little shade or hiding places for your fish. (You should be able to find some old threads using the search function.)

Finally, dyeing your pond water is a common option on Pond Boss as a means to suppress the growth of filamentous algae. Especially, when the water is so clear that the algae is capable of starting its growth on the bottom in "deep" water. I do not know how much effect dyeing the water will have on your zooplankton food chain. Perhaps you could start a new thread on that specific option if you want further info, and some of the experts might chime into your thread.

A 1.25 acre quarry pond sounds like a beaut' to me. Good luck with your pond improvements!