We present a set of boundary conditions for solving the elliptic equations in the initial data problem for space-times containing a black hole, together with a number of constraints to be satisfied by the otherwise freely specifiable standard parameters of the conformal thin sandwich formulation. These conditions altogether are sufficient for the construction of a horizon that is instantaneously in equilibrium in the sense of the isolated horizons formalism. We then investigate the application of these conditions to the initial data problem of binary black holes and discuss the relation of our analysis with other proposals that exist in the literature.