We present a detailed investigation of the specific heat in Ca$_3$(Ru$_{1-x}M_x$)$_2$O$_7$ ($M$ = Ti, Fe, Mn) single crystals. With different dopants and doping levels, three distinct regions are present, including a quasi-2D metallic state with an antiferromagnetic (AFM) order formed by ferromagnetic bilayers (AFM-$b$), a Mott insulating state with G-type AFM order (G-AFM) and a localized state with a mixed AFM-b and G-AFM phase. Our specific heat data provide deep insights into the Mott transitions induced by Ti and Mn dopings. We observed not only an anomalous large mass enhancement but also an additional term in the specific heat i.e. $Cpropto T^2$ in the localized region. The $Cpropto T^2$ term is most likely due to the long-wavelength excitations with both FM and AFM components. A decrease of Debye temperature is observed in the G-type AFM region, indicating a lattice softening associated with the Mott transition.
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