As long as you axiomatize set theory in first-order logic, the answer to your question is no. The axioms would be consistent with each finite subset of the following set of sentences involving a new constat constant symbol $c$: "$c$ is a natural number" and "$c\neq n$" for each (standard name of a) natural number $n$. By compactness, there would be a model of the axioms plus all of these sentences, and in that model $c$ would denote a nonstandard natural number.
On the other hand, if you're willing to go beyond first-order logic, then the answer to your question is yes. For example, in second-order logic, you can express the induction axiom as a single sentence and be confident that "set" really manes means arbitrary set (not "internal set" or anything like that). In other words, once you're sure that "set" has its intended meaning, the induction principle guarantees that "natural number" also has its intended meaning. (To me, this doesn't look very helpful, since the intended meaning of "set" seems more complicated than the intended meaning of "natural number".)
For another example, if you're willing to use infinitary logic, then you can formulate the axiom "every natural number is equal to 0 or to 1 or to 2 or to 3, or ..."
