It's not true that the order of words could be anything any more than it's true that "Time flies like an arrow" could be understood in all the 11 different interpretations that one can read into it. Latin is a language that has a syntax that is connected with intonation - it's not some unconnected jumbling of piecemeal English translations that can be put together in any arbitrary way to arrive at any arbitrary but theoretically possible meaning. Poetic speech can lead to various transformations to the unmarked word order, but never to the effect that the result could mean anything and nothing, especially when disambiguated by reading it with appropriate breaks and intonation. These transformations have their own rules and for the most part follow a formulaic/traditional/idiomatic pattern such that given enough fluency and experience, one can often spot them at first sight. Sense alone is usually enough to remove any remaining ambiguity. Anyone who forgets about sense and syntax when dealing with language forgets they're dealing with language, or else forgets that they're a human and not a psittacine. Playing "buffalo buffalo buffalo" is fine as long as one doesn't forget they're just playing a metalinguistic game.
The word order you give is close enough to the default one, presents no ambiguity whatsoever and means what you intended it to. A more neutral word order to me would be agricolae fīlia aquās silvae amat - which mirrors exactly the English "[the farmer's daughter] loves [the waters of the forest]". Using the adjective silvestris is perfectly fine too, and can come in handy when there's real ambiguity involved - and is also more idiomatic.
If you make it the plural fīliae agricolae, it's still clearly the subject (not fīliās) and there's still only one way this subject makes sense outside of some exceptional context (and fīliae would still tend to come last). If you had to say "the daughter's farmers", i.e. "the farmers that the daughter talked about", you could for instance use a demonstrative pronoun and emphatic word order: [agricolae istī] fīliae. Basically Latin has many homophonic (same-sounding) forms, but it has very flexible syntax, arguably to compensate for this. It's mostly in exercises with no context at all that you can't tell what goes with what, but such exercises are often designed to confuse you, and possibly to make a point about the difficulty of Latin. Real Latin is designed to be understood.