We construct a topological Chern-Simons sigma model on a Riemannian threemanifold M with gauge group G whose hyperkähler target space X is equipped with a G -action. Via a perturbative computation of its partition function, we obtain new topological invariants of M that define new weight systems which are characterized by both Lie algebra structure and hyperkähler geometry. In canonically quantizing the sigma model, we find that the partition function on certain M can be expressed in terms of Chern-Simons knot invariants of M and the intersection number of certain G -equivariant cycles in the moduli space of G -covariant maps from M to X . We also construct supersymmetric Wilson loop operators, and via a perturbative computation of their ex...