The invention relates to a compressor unit, in particular, for submarine application, comprising an electric motor. The transported medium for compression, in particular, natural gas for transport, not only frequently contains various aggressive chemical compounds but is also carrier of various condensates which hinder compression and in particular lead to increased wear of the compressor. On assembly aggressive sea water can also enter the compressor unit. The invention provides a solution to the above, wherein the rotation axis is arranged vertically during operation and the housing comprises a drain at the lower axial end. The invention further relates to an assembly method for a compressor unit, in which the compressor unit is filed above water with an incompressible fluid, transported to a submarine operating position, connectors are connected to the inlet and the outlet and the fluid removed from the compressor unit through the drain.