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If you have a filter and pump - Change the filter media and run it continuously for a couple of days or a week. If you don't have a filter/pump system - visit a local pond/ nursery to see if they can help you set one up.
If you have fish make sure you screen the intake.
Good luck - Bill E

Generally rocks are used to anchor a pond liner and to create a natural ponding effect.
Here is where you can be creative with ground cover plants and perennials to create a lovely garden.
Here are some links to help you get started.

https://www.gardeningknowhow.com/garden-how-to/projects/how-to-build-a-small-pond.htm
https://www.gardeningknowhow.com/ornamental/water-plants/wgen/popular-pond-plants.htm

I too have a small garden pond that gives me such pleasure and grief!

Do you run a pump and filter in your pond?
After cleaning the largest of litter out of the water, relying on the filter to clean the finest material is a process.
The filter needs flushing every day during the first days of cleaning, then less often.
Slowly the finest material is removed from the water.
Patience and a good pond filter is recommended from my experience.
Here are some articles with more information.

https://www.gardeningknowhow.com/ornamental/water-plants/wgen/cleaning-garden-ponds.htm
https://www.gardeningknowhow.com/composting/ingredients/pond-scum-garden-fertilizer.htm
https://www.gardeningknowhow.com/plant-problems/weeds/duckweed-control.htm

This link will help you.

https://www.gardeningknowhow.com/houseplants/hpgen/fish-bowl-plants.htm

The problem with using coco liner for this application will be that it will rot over time. This will lead to a nasty mess. There are many things that will be useful for your application, though.

Apart from pebbles, you can use Grow Stone, clay pellets, or any hydroponic medium.

Now, if you intend to keep the water changed, and keep an air pump to keep it from getting stagnant, then it will be ok to use a coco liner. It will be important to treat this as a hydroponic system with weekly, or at the very least, monthly cleanings though.

Here are some ideas for creating water gardens that you may find useful: https://www.gardeningknowhow.com/ornamental/water-plants/wgen/pond-and-water-gardens.htm

Do you have surface plants, too, such as water lilies? You can cover up to 50 percent of the surface water with lilies. The shade will reduce the algae and the fish will appreciate it. Also, fertilize plants as little as possible and don't overfeed the fish. Excess nutrients will only feed the algae.

https://www.gardeningknowhow.com/ornamental/water-plants/wgen/algae-removal.htm