A well pump assembly has a main pump suspended on a string of production tubing within casing in a well. A charge pump is located below the main pump. An annular sealing element between the charge pump intake and the charge pump discharge seals between the charge pump and the casing. A motor is coupled with the main pump and the charge pump. A bypass member has an open upper end above the main pump intake and a lower end above the sealing element. The bypass member defines a flow path from the discharge of the charge pump upward past the main pump intake, then downward to reach the main pump intake. The bypass member may be a bypass riser extending alongside the main pump, or it may be a shroud surrounding the main pump.