A variable buoyancy subsea running tool for use with subsea transportable devices, such as a tree cap. The buoyancy of the running tool may be varied through fluid or gas displacement in one or more containers. Alternatively, the running tool may be configured with a buoy that has static buoyancy, with the buoyancy of the running tool being varied through the addition of a counterweight. The running tool can be used to install or uninstall a tree cap on a subsea tree. Installation of a tree cap may be actuated by a remotely operated vehicle. Additionally, the running tool may be moved by a remotely operated vehicle and may have additional features such as a position locator device.