Skjern Å (running W), 55°53' N 9° 24' E" to 55°55' N 8° 23' E", 4th longest stream in Denmark, but most volumnous by a little bit.
Starts in Tinnet Krat 70 m above sea level and runs 94 Km West to Fuglsang in Ringkøbing Fjord, drains 2100 Sq Km, falls 70 m from start to end, 36,6 m³/s water runds through it.

Gudenå (running E), 55° 54' 04" N 09° 24' 26" E to 56° 28' N 10° 03' E, longest stream in Denmark, runs through some beautiful nate and a lot of lakes BTW.

Starts in Tinnet Krat as well, only a few 100 m from Skjern Å's spring and 65 m above sea level, and runs 176 Km East and NE to Randers Fjord. Drains 2643 km² at 36,6 m³/s (same as Skjern Å, though the latter is supposedly more volumnous). Runs through the lakes Mossø and Silkeborg søerne (plus some artificial ones which were not there in The Iron Age) and also drains Skanderborgsøerne). Gudenåen is the only stream classed as river in Denmark, and up until 19th century was also significant as a way for barges to go quite far upstream and thus ease transportation. Something Gudenå hinders quite a lot with its many lakes.

At any rate the major prehistoric route up through Jylland "Hærvejen"/"Oksevejen" (Army or War Road/ Ox Road- from 15th cenuty onwards it was used to export cattle to N. Germany). passes the spring of both streams in Tinnet Krat, and should one wander it, one can also meet many remains of dikes etc (like Offa's and Danevirke, but significantly shorter). This track probably streches about as far back as habitation in Denmark, IE 15.000 or so years.

I can do some research as to which of them hindered transport the most in old times, but it seems safe from its length and many lakes that it is Gudenåen, though Skjern Å supposedly has more volume...