You have to understand that in the pre-classical era, Roman people had minor god cults throughout their small villages, and the Greeks did the same thing. The cults beliefs did some traveling over time, and reasonable people slowly began piecing together a shared mythos.
Over time, as the Greeks pulled together their culture into a power structure of loosely associated city-states, their religious cults from dozens and dozens of villages all were glued together into a more cohesive pantheon.
Romans then adopted and 'latinized' the Greek pantheon, mixing in several of their own superstitions and cults.
This means you will have a God of creation and a God of that pond over there, which might have later been rationalized into a nymph.
EDIT:
It's much the same in the Abrahamic religions. Yahweh was the god of storms/thunder, sort of second or third in command to El, had a wife etc. Later he was given domain over war and then later promoted to the one true God.
You can see small remnants of this in the Bible, in the conflicts with Baal (another diety of the pantheon) especially (theorized to be some of the oldest stories in the Bible). Yahweh often uses thunder and lightning in his signs, and in older records mention is made of his wife/children etc.
Before things were commonly written down and literacy was common Religious beliefs were messy, constantly adapting and re-adapting to changing times, rulers, and encounters with other systems of belief.