A fluid separation system is provided for separating wellbore fluids into production fluids and non-production fluids. The system includes a separator adapted for transmitting mechanical power between a drive motor and at least one pump. The separator includes one or more separation units, such as hydrocyclone separators. A drive train traversing the separator is interfaced with drive elements, such as a submergible electric motor, and driven elements such as an injection or production pump. Wellbore fluids are channeled through the separator in either a push-through or pull-through manner. Production fluids are then transferred from the separator to the production pump for removal from the well. Non-production fluids are transmitted from the separator either to the injection pump for reinjection into a subterranean discharge zone, or directly into the discharge zone from the separator. The drive train elements traversing the separator are supported by antifriction bearings in interface plates on either end of the separator. The ability to transmit mechanical power through the separator facilitates assembly of pumping system components in various configurations as well as piping fluid communication paths between the pumping system components.