Metropolitan Spain, limón is lemon and lima is lime; limonada natural is made with lemon and water (sugar optional, and if so just enough to take the worst bite off), limonada as a soda is the one that’s yellow and acidic. I already knew before leaving the country that in other places it can be made with limes and that there’s places where the term can mean other kinds of “watered down cold juice” (such as that one with lime and coconut Leo Bloom mentioned) or of soda, but I can’t remember when or where did I learn that. My guess is that it’s more likely to be made with whichever is more available locally: here, limes are exotic and coconut is reserved for slices at the fairground or for cake decorations, whereas orange and lemon trees are found in any area that’s not too wet for them (so, most of the country).
Out of curiosity I’ve checked RAE: their definitions talk about limones having yellow skin and flesh, with limas having yellow skin and green flesh. No indication of regional variations. For limonada, they say “(adj.) lemon colored” and “(noun) a drink made from water, sugar and lemon juice” - I guess the soda is supposed to fall under the first definition, and the second one depends on which fruit do you call what.
I’m guessing a Spanish OED thing?