Following the approach of Ding and Frenkel [Comm. Math. Phys. 156 (1993), 277-300] for type $A$, we showed in our previous work [J. Math. Phys. 61 (2020), 031701, 41 pages] that the Gauss decomposition of the generator matrix in the $R$-matrix presentation of the quantum affine algebra yields the Drinfeld generators in all classical types. Complete details for type $C$ were given therein, while the present paper deals with types $B$ and $D$. The arguments for all classical types are quite similar so we mostly concentrate on necessary additional details specific to the underlying orthogonal Lie algebras.