The shuffle lattice was introduced by Greene in 1988 as an idealized model for DNA mutation, when he revealed remarkable combinatorial properties of this structure. In this paper, we prove an explicit formula for the $M$-triangle of the shuffle lattice, a bivariate refinement of the characteristic polynomial, as conjectured by McConville and Mühle in 2022, and find a relation between the $M$-triangle and the $H$-triangle, a bivariate refinement of the rank generating function.