The canal is used for a combined farm irrigation and power generation scheme and is operated by Rangitata Diversion Race (RDR) Management.
The fish screen system is the largest and most complex ever built in New Zealand and among the largest in the world.
If they go with the flow the fish find their way back into the river within about two minutes.
"It's designed to help protect both the sports fishery, which is the salmon and trout, mainly salmon, and the native fish of which there's a variety of species," says RDR Management's Tony McCormick, who has overseen the project.
"Testing is going to be very challenging.
"We're still refining that process and we'll be doing close examinations for fin damage and that sort of thing using test fish, that we'll release and then capture."
Monitoring fish health will be conducted with support from Fish & Game "... and the local anglers who in a way sort of initiated this project with their discontent," McCormick says.
Since RNZ's Country Life visited the fish screening facility it has now gone under water and is successfully diverting fish back into the Rangitata River.