We study to what extent Wilson lines in heterotic Calabi-Yau compactifications lead to non-trivial H-flux via Chern-Simons terms. Wilson lines are basic ingredients for Standard Model constructions but their induced H-flux may affect the consistency of the leading order background geometry and of the two-dimensional worldsheet theory. Moreover H-flux in heterotic compactifications would play an important role for moduli stabilization and could strongly constrain the supersymmetry breaking scale. We show how to compute H-flux and the corresponding superpotential, given an explicit complete intersection Calabi-Yau compactification and choice of Wilson lines. We do so by identifying large classes of special Lagrangian submanifolds in the Calabi-Yau, understanding how the Wilson lines project onto these submanifolds, and computing their Chern-Simons invariants. We illustrate our procedure with the quintic hypersurface as well as the split-bicubic, which can provide a potentially realistic three generation model.