We present an extensive density functional theory analysis of the structural, electronic, and magnetic properties of isolated 3d transition metal adatoms (from Ti to Co) adsorbed on free-standing and Ni(111)-supported graphene. We discuss how the energetics of different adsorption sites is influenced by the filling of d-orbital filling across the 3d series and identify a direct correlation between the adatom-graphene distance and the degree of charge transfer. The presence of the Ni substrate is found to have stronger impact on the adatoms at the end of the series, leading to modifications of the preferred adsorption site, charge transfer, and spin properties. The magnetic exchange coupling between the spin of the adatom and the Ni magnetization changes as a function of the adatom both in sign (preferred antiferromagnetic exchange for Ti, V, and Cr, and ferromagnetic alignment for the other elements) and in magnitude (from 90 meV for Mn to ≈10 meV for Fe an Co).