We completely classify Cartan subalgebras of dimension drop algebras with coprime parameters. More generally, we classify Cartan subalgebras of arbitrary stabilised dimension drop algebras that are non-degenerate in the sense that the dimensions of their fibres in the endpoints are maximal. Conjugacy classes by an automorphism are parametrised by certain congruence classes of matrices over the natural numbers with prescribed row and column sums. In particular, each dimension drop algebra admits only finitely many non-degenerate Cartan subalgebras up to conjugacy. As a consequence of this parametrisation, we can provide examples of subhomogeneous C*-algebras with exactly n Cartan subalgebras up to conjugacy. Moreover, we show that in many dimension drop algebras two Cartan subalgebras are conjugate if and only if their spectra are homeomorphic.