Interesting, does the subspeciation of brook trout and arctic char in some areas reflect the headwater species differences?
I couldn't tell you in that specific case. But in general, species that inhabit headwaters become adapted to them, and that is usually associated with changes that do not serve them well when they try to disperse from headwater A to headwater B via big water (rivers, marshes, etc) that connects them. This headwater isolation leads to genetic isolation, and thus speciation, especially when allopatry is used as a major "character" to warrant species status. Of course, this period you're interested in involved rapid changes in base flows, which facilitated headwater captures and inter-basin exchanges that lead to some big head scratchers.
Allopatry is the reason there are so many species of darters, because as Todd has pointed out, you can think of riffles as islands and once that proto-Ammocrypta-Etheostoma-Nothonotus ancestor lost that swim bladder, it got really hard to disperse through big water connecting various riffle habitats. However, the basal Percina still have a swim bladder (to varying degrees) and other ancestral characters that still allow them to disperse through larger systems, and is likely the reason many big river Percina have such large distributions (compared to most Etheostoma). Of course, each species has differing dispersal capabilities, but you can draw some rough lines to help understand fish distributions.