I'm also going to disagree with Melinde-Mari. Fish swim in rivers. Ducks swim on rivers.

It will still be "in" the river Because the duck is swimming so it inclines that something in this case the duck is partially or fully 'in' the water also because you're telling us 'where' the duck is swimming. With "Swimming" it will always be "in" that is used, but ~ You could say the duck "float's on water" but as soon as saying 'where' it'll change to "in" "The duck is floating in the river... on the water..."

I would say "on" as it implies on top as ducks swim on the surface. "In" implies underneath the surface like another answer said like fish.

I'm going to disagree with Melinde and go with "on", especially as ducks swim on the river but I can also imagine "in" would work well. So both....

You could use either but the more correct expression is swim IN the water. Also, float ON the water. The duck swims in the river. The duck floats on the river.