Large-Eddy Simulations (LESs) and experiments were employed to study the influence of water depth on the hydrodynamics in the wake of a conical island for emergent, shallow, and deeply submerged conditions. The Reynolds numbers based on the island's base diameter for these conditions range from 6500 to 8125. LES results from the two shallower conditions were validated against experimental measurements from an open channel flume and captured the characteristic flow structures around the cone, including the attached recirculation region, vortex shedding, and separated shear layers. The wake was impacted by the transition from emergent to shallow submerged flow conditions with more subtle changes in time-averaged velocity and instantaneous flow structures when the submergence increases further. Despite differences in the breakdown of the separated shear layers, vortex shedding, and the upward flow region on the leeward face (once the cone's apex is submerged), similar flow structures to cylinder flow were observed. These include an arch vortex tilted in the downstream direction and von Karman vortices in the far-wake. Spectra of velocity time series and the drag coefficient indicated that the vortex shedding was constrained by the overtopping flow layer, and thus the shedding frequency decreased as the cone's apex became submerged. Finally, the generalised flow structures in the wake of a submerged conical body are outlined.