In the Chicago Sanitary and Ship Canal there is no physical barrier. An electrical barrier was originally put in as a pilot barrier about 10 years ago to prevent the spread of round goby into the Mississippi River. It was built too late to do that, but then as the threat of invasive species came the other way, with Asian carp, they realized it had the potential to prevent Asian carp from moving into the Great Lakes.
Because it was only a demonstration barrier, there were concerns that barrier failure might lead to times when the fish could actually get by, so they built a second barrier which is now operational. There are plans to build a third within this area south of Chicago. An electrical barrier has been shown to be highly effective. They've done trials where they've tagged surrogate species, such as common carp, that they know will not go through the barrier. It appears to be quite effective.
I would suggest that no barriers are 100% effective. When you hear about physical barriers, what they're talking about is physical separation. You need to understand that, essentially, they're going to fill in the canal to completely separate the watersheds.
There is also talk about ecological separation, where you prevent the organisms from mixing. That's what this barrier's doing, at least with fish.