Let M be a connected, closed, oriented three-manifold and K, L two rationally null-homologous oriented simple closed curves in M. We give an explicit algorithm for computing the linking number between K and L in terms of a presentation of M as an irregular dihedral three-fold cover of $$S^3$$
S
3
branched along a knot $$\alpha \subset S^3$$
α
⊂
S
3
. Since every closed, oriented three-manifold admits such a presentation, our results apply to all (well-defined) linking numbers in all three-manifolds. Furthermore, ribbon obstructions for a knot $$\alpha $$
α
can be derived from dihedral covers of $$\alpha $$
α
. The linking numbers we compute are necessary for evaluating one such obstruction. This work is a step toward testing potential counter-examples to the Slice-Ribbon Conjecture, among other applications.