An explicit isomorphism between the $R$-matrix and Drinfeld presentations of the quantum affine algebra in type $A$ was given by Ding and I. Frenkel (1993). We show that this result can be extended to types $B$, $C$ and $D$ and give a detailed construction for type $C$ in this paper. In all classical types the Gauss decomposition of the generator matrix in the $R$-matrix presentation yields the Drinfeld generators. To prove that the resulting map is an isomorphism we follow the work of E. Frenkel and Mukhin (2002) in type $A$ and employ the universal $R$-matrix to construct the inverse map. A key role in our construction is played by a homomorphism theorem which relates the quantum affine algebra of rank $n-1$ in the $R$-matrix presentation with a subalgebra of the corresponding algebra of rank $n$ of the same type.