Two new mixed-valent triple perovskites, Ba3MRU2O9 (M = Li, Na), were grown from reactive hydroxide fluxes. They crystallize in the hexagonal space group P6(3)/mmc, where Ru(V) and Ru(VI) are disordered on only one crystallographic site. Upon cooling, single crystals of Ba3NaRU2O9 undergo a complex symmetry-breaking structural transition at ca. 225 K from room-temperature hexagonal symmetry to a low-temperature orthorhombic symmetry, space group Cmcm. Accompanying this structural transition is a rather abrupt decrease in the magnetic susceptibility at 210 K followed by a steady decrease in the susceptibility with decreasing temperature. Interestingly, the lithium analogue does not display any structural transition down to 100 K. The structural transition in Ba3NaRU2O9 generates three crystallographically unique Ru sites in the low-temperature structure as compared to only one distinct site in the room-temperature structure. On the basis of an analysis of the Ru-Ru distances in the face-sharing bi-octahedra, the structural transition also appears to involve charge ordering of Ru(V) and Ru(VI), causing all Ru(V) to occupy one set of bioctahedra and all Ru(VI) to occupy another set.