We provide a new framework for the study of fl‡uid ‡flows presenting complex uncertain behavior. Our approach is based on the stochastic reduction and analysis of the governing equations using the dynamically orthogonal field equations. By numerically solving these equations we evolve in a fully coupled way the mean fl‡ow and the statistical and spatial characteristics of the stochastic fl‡uctuations. This set of equations is formulated for the general case of stochastic boundary conditions and allows for the application of projection methods that reduce considerably the computational cost. We analyze the transformation of energy from stochastic modes to mean dynamics, and vice-versa, by deriving exact expressions that quantify the interaction among different components of the fl‡ow. The developed framework is illustrated through specifi…c fl‡ows in unstable regimes. In particular, we consider the ‡flow behind a disk and the Rayleigh–-Bénard convection, for which we construct bifurcation diagrams that describe the variation of the response as well as the energy transfers for different parameters associated with the considered ‡flows. We reveal the low-dimensionality of the underlying stochastic attractor.