  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 classifying 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.
