The lyrics: https://earth-colors.dreamwidth.org/14442.html
This line 川面の上を雲が流れる is translated as "Clouds passing over a flowing river".
川面 is already the river's surface, so would 川面の上 be "that which is above the river's surface"? (which makes sense to me, since the next line indicates the speaker was looking at a reflection all along (and a river's surfaces reflects what is above it) and since that (the reflection) is moving, it was translated as a flowing river)
Also, this was the first time I encountered the verb 流れる. Jisho.org tells me that it is intransitive. Jisho provides this example セーヌ川はパリを流れている, here with the を after パリ, Paris is what the Seine flows through. Another example on Jisho is ...水がこの川にも流れていた, here with が after 水, it was water that was also being washed away in this river.
If I apply these deliberations to 川面の上を雲が流れる, it is "that which is above the river's surface" which is flown through and the clouds that are washed away. Since 流れる is said to be intransitive, I see this as two sentences 川面の上を流れる and 雲が流れる. I am far out of my depth here.
1.) What is happening here, how can 流れる be in a sentence that has を and が?
2.) Should 川面の上を雲が流れる be seen as two sentences?