The river border between Belgium and the Netherlands, in Dutch 'de Maas' and in French called 'La Meuse'.
The stretch measured in a straight line is about 19.5 mile, about 31.5 km, (Google maps) but because of the nature of the river much longer by water, and also going by road will take much longer.
That is between Maasbracht, the Netherlands - Kessenich, Belgium and Lanaken, Belgium - Maastricht, the Netherlands.
Ferry crossing 'de Maas' at Grubbenvorst and Velden
Photo released to public domain, by Gouwenaar.
There has been a recent border adjustment as the river had changed its bedding but the official border was still on its fixed paper line. A part of the border on the Dutch side of the river was officially still Belgium and while the people just walked over the border, Belgium police and other officials had to apply for permission to pass the Netherlands into the part of Belgium. You can find more about it in English language newpapers and online versions, as far away as NY Times, this Irish one comes with several photos.
As you can read in those news snippets, it is easy and allowed to cross the river by small craft, no border officials and also no or not much in the way of border markings, depending on where of the river you happen to cross. There might be some ancient markers from where there has been an official border crossing over the centuries, it is only in the last 40 years that there are no border checks between Belgium and the Netherlands, I am not even sure how long myself.
The border crossing of the river Rhine (Rijn) from Germany into the Netherlands takes about 4.67 miles, about 7.5 km (measuring curtecy of Google maps) and due to the nature of the river, pleasure boating is less encouraged, but still possible and allowed.
Spijk in the Netherlands is along one side the river as is Tolkamer, Kleve in Germany on the other. Border checks did continue here till the start of the Schengen zone allowed for check-free crossings.
If you go to 51.846848, 6.154735 on google maps and use street view you can see the river, as it was the moment their camera vehicle came past.
Rhine with groynes near Tolkamer, Netherlands.
By Gouwenaar (Own work) [Public domain], via Wikimedia Commons
There is a roughly 2.5 mile, 4 km stretch of border north of there, about as far north as you can go along that border.
Due to the laws in Germany, or at least to the way Google streetview implements it, I can not give you a few of the water at the actual border, this is the nearest I can get in the Netherlands: 53.183672, 7.203187
The town is called Bad Nieuweschans, the Netherlands, on the other side of the border you can find Bunde, Germany. The water there looks like man made, but it might be a canalized bit of river as well. Again, as far as I can see no rules against pleasure boats, but I am not sure, not having been there. I know it is accessible by car/foot as my brother has visited the area once.
That is just three on the border of the Netherlands, I am sure you can go around other Schengen borders to find more. Use a 'walk around' option with the online map, wherever possible, to check out the nature of the borders.
I agree with the other answer, if you want to see signs of the border in the water, better check where the water crosses the border rather than being the border. And the more recent the crossing was guarded, the more likely you will find signs of guarding.
And the more defended the border was, the more likely you will find proof in the river even after years.
In that respect, you might want to check out where used to be the border between the two Germanies. No border anymore, when it became a border between two political blocks it was one nation with all kind of waterways crossing the line, and there is no reason to take out all signs of having been a border unless it is big enough for serious boat traffic.
But I am not sure it fits your requirements as you do mention it being an actual national border.