Chip them? I mean it wouldn't be that hard. You could also use genome tracing (registered genome lines with the Fish and Game department) That test would take a bit longer but with spot enforcement you'd probably keep compliance acceptably high.

I wonder if this is counterproductive. In California, there are plenty of endangered aquatic species, and if people could legally buy and own captive-bred individuals, then perhaps there could be more native species kept as pets and fewer potentially invasive species.

Even better: maybe regular people with ponds, etc could (easily) get permission to stock them with species that actually belong where they live. And maybe the species would become less endangered.

any number of ways? a simple bill of sale from a legal distributor?

The super-expensive ones are bred for outlier traits like being bright red, platinum white, etc. It seems unlikely that ones harvested from the wild could compete.