Methods of forming bonded semiconductor structures include providing a substrate structure including a relatively thinner layer of material on a thicker substrate body, and forming a plurality of through wafer interconnects through the layer of material. A first semiconductor structure may be bonded over the thin layer of material, and at least one conductive feature of the first semiconductor structure may be electrically coupled with at least one of the through wafer interconnects. A transferred layer of material may be provided over the first semiconductor structure on a side thereof opposite the first substrate structure, and at least one of an electrical interconnect, an optical interconnect, and a fluidic interconnect may be formed in the transferred layer of material. A second semiconductor structure may be provided over the transferred layer of material on a side thereof opposite the first semiconductor structure. Bonded semiconductor structures are fabricated using such methods.