Divalent ions can mediate condensation of highly charged biological macromolecular assemblies by producing attractions and suppressing repulsions between like-charged structures. Combining small-angle x-ray scattering with x-ray fluorescence techniques has allowed us to directly and quantitatively probe the correlation between the structural transitions of like-charged biomolecules and the density of counterions bound to the supramolecular structures. We report here on the dependence of this attractive electrostatic regime on counterion concentration and type (i.e. ion-specific effects) for two different in vitro systems: tau protein-coated microtubules in dissipative, out-of-equilibrium conditions and DNA molecules confined to two dimensions by cationic liposomes at equilibrium. The functional implications of these ion-mediated transitions in biological assemblies are poorly understood, creating a need for further research.