We study stochastic thermodynamics of overdamped Brownian motion in a flowing fluid. Unlike some previous papers, we treat the effects of the flow field as a nonconservational driving force acting on the Brownian particle. This allows us to apply the theoretical formalism developed in a recent paper for general nonconservative Langevin dynamics. We define heat and work both at the trajectory level and at the ensemble level, and prove the second law of thermodynamics explicitly. The entropy production is decomposed into a housekeeping part and an excess part, both of which are non-negative at the ensemble level. Fluctuation theorems are derived for the housekeeping work, the excess work, and the total work, which are further verified using numerical simulations. A comparison between our theory and an earlier theory by Speck et al. [Phys. Rev. Lett. 100, 178302 (2008)0031-900710.1103/PhysRevLett.100.178302] is also carried out.