  For configurational changes of soft matter systems affected or caused by
external hydrodynamic flow, we identify applied work, exchanged heat, and
entropy change on the level of a single trajectory. These expressions guarantee
invariance of stochastic thermodynamics under a change of frame of reference.
As criterion for equilibrium \textit{vs.} nonequilibrium, zero \textit{vs.}
nonzero applied work replaces detailed balance \textit{vs.} nonvanishing
currents, since both latter criteria are shown to depend on the frame of
reference. Our results are illustrated quantitatively by calculating the large
deviation function for the entropy production of a dumbbell in shear flow.
