Non-conservation of magnetic neutron scattering from the six-layer hexagonal perovskite Ba3CaRu2O9 on cooling reveals that (Ru5+)2 dimers form nonmagnetic spin-singlet ground states. This is in contrast to Ba3BRu2O9 (B=Co or Ni) analogues which display long range spin ordered ground states containing antiferromagnetic (Ru5+)2 dimers (Lightfoot and Battle 1990 J. Solid State Chem. 89 174). Dimer formation is weakly coupled to the lattice, resulting in an excess  microstrain broadening of diffraction peaks at low temperatures. Non-conservation of magnetic neutron scattering is also observed around the charge ordering transition in Ba3NaRu2O9 showing that the ground state structure is coupled to spin-singlet formation in charge ordered Ru2O9 dimers.