We used EXAFS and DFT calculations to investigate the structure of [Ru(bpy)(AP)₄]²⁺ and [Ru(bpy)₂(AP)₂]²⁺ (bpy=2-2'-bipyridyne, AP=4-aminopyridyne) in aqueous solution (10 mM). These derivatives are of potential interest since, upon direct irradiation, they can form reactive aqua-species able to bind to macromolecules. An attempt has been made to determine with EXAFS the structure of the photodissociation product of the [Ru(bpy)₂(AP)₂]²⁺ complex, where a water molecule fill the coordination vacancy left by an AP ligand resulting in [Ru(bpy)₂(AP)(H₂O)]²⁺. Unfortunately, co-presence in the experimental sample of both original and photodissociated complexes, causes the failure of the analysis. This failure was due to the structural complexity of both systems and to the similarity in their EXAFS signals. This work underlines the potentialities and the limits of EXAFS spectroscopy when dealing with highly diluted samples where the local environment of the adsorbing atom is characterized by structured ligands: the local environment of Ru is correctly reproduced when dealing with homogeneous samples, while the co-presence of two or more different species makes the data analysis highly critical.