In this paper we develop the theory of cyclic flats of $q$-matroids. We show that the lattice of cyclic flats, together with their ranks, uniquely determines a $q$-matroid and hence derive a new $q$-cryptomorphism. We introduce the notion of $\mathbb{F}_{q^m}$-independence of an $\mathbb{F}_q$-subspace of $\mathbb{F}_q^n$ and we show that $q$-matroids generalize this concept, in the same way that matroids generalize the notion of linear independence of vectors over a given field.