Even if you are trying to repopulate a species in a freshwater system your source fish are going to be from the same river basin as to where you plan to repopulate regardless if the project is a captive breeding one or a simple collection and release effort.
Why? Genetics.
For example, even within a river system you can have 3 populations with "identically" looking fish, though there maybe some variation in color or lateral line scale counts but if you look at the genetic composition those 3 populations are independent of one another and the question is then raised:
How many species are present?
Here is an example of something simple having a major impact:
http://www.invasivespeciesinfo.gov/aquatics/didymo.shtml
In some areas felt boot waders are no longer allowed because it has been proposed that if one picks it up in one affected stream and fishes in another unaffected one it can spread.