I think most likely he jumped. I've had various fish jump right out of my aquarium, even with the hood on it! They got out in the small opening where the tubing was inserted. Sometimes they jump because there are parasites, sometimes because of an ammonia build-up, sometimes because they're startled by something -- or sometimes just for the sheer joy of jumping.

Plants do well at filtering out toxins, especially when you're not overstocked, but if you're curious, the easy way to check the water quality would be to get a testing kit.

Most often fish jump out because the water is toxic. You need to get a test kit and find out what is wrong. Water clarity has nothing to do with it. My swimming pool is perfectly clear and would quickly kill any fish put in it.