Based on the coupled problem of time-dependent fluid–structure interaction, equations for an appropriate adjoint problem are derived by the consequent use of the formal Lagrange calculus. Solutions of both primal and adjoint equations are computed in a partitioned fashion and enable the formulation of a surface sensitivity. This sensitivity is used in the context of a steepest descent algorithm for the computation of the required gradient of an appropriate cost functional. The efficiency of the developed optimization approach is demonstrated by minimization of the pressure drop in a simple two-dimensional channel flow and in a three-dimensional ducted flow surrounded by a thin-walled structure.