You nailed it on the head with the "flowing in and out" part. If any of the fish farm just have a hole in the ground, without any water leaving site (example would be recycling of water usages), then the regulations would not have any teeth. Unfortunately, the fish farms are tapping into the water of the U.S., and discharge the water with or without proper monitoring. So...Dept of Fish and Game got strict on these farms. It's understandable, since what the farms release will harm the downstream waters, ecologically, and health wise. I hate getting hammered with big fees and fines too, but we need to clean our craps up and not leave our craps to be dealt with by others downstream from us, or rather, leave it for the next generations to take care of our messes.
By the way, I'm not a tree huger
I'm a scientist that knows more than 95% of the people about water quality and environmental impacts due to urbanization. If you have a few days to spare, I may turn your average thinking to a tree huger's mindset
Scary thought isn't it?