I've tried to look here:
But it's not clear to me. Also I don't understand why über-queren should literally translate as over crossing.
Can you help me?
Überqueren requires that you cross something that's physically located beneath you. Take
Queren describes a traversal where the movement is roughly perpendicular to a (often implicitly) contextually defined preferred orientation of what is being crossed.
Both verbs indeed mean "to cross" (i.e. a river). The "über" can be used to indicate two things in the sentence "Wir überquerten den Fluss":
So without an extra indication on the means how you got over the river, the two terms can be used exchangeably, except that you cannot say "überqueren" if you meant to go under it.