We present an explicit formula for the transition matrix C from the type BC n Koornwinder polynomials P (1 r) (x|a, b, c, d|q, t) with one column diagrams, to the type BC n monomial symmetric polynomials m (1 r) (x). The entries of the matrix C enjoy a set of four terms recursion relations. These recursions provide us with the branching rules for the Koornwinder polynomials with one column diagrams, namely the restriction rules from BC n to BC n−1. To have a good description of the transition matrices involved, we introduce the following degeneration scheme of the Koornwinder polynomials: P (1 r) (x|a, b, c, d|q, t) ←→ P (1 r) (x|a, −a, c, d|q, t) ←→ P (1 r) (x|a, −a, c, −c|q, t) ←→ P (1 r) x|t 1/2 c, −t 1/2 c, c, −c|q, t ←→ P (1 r) x|t 1/2 , −t 1/2 , 1, −1|q, t. We prove that the transition matrices associated with each of these degeneration steps are given in terms of the matrix inversion formula of Bressoud. As an application, we give an explicit formula for the Kostka polynomials of type B n , namely the transition matrix from the Schur polynomials P (Bn,Bn) (1 r) (x|q; q, q) to the Hall-Littlewood polynomials P (Bn,Bn) (1 r) (x|t; 0, t). We also present a conjecture for the asymptotically free eigenfunctions of the B n q-Toda operator, which can be regarded as a branching formula from the B n q-Toda eigenfunction restricted to the A n−1 q-Toda eigenfunctions.