A subsea pumping assembly locates on a seafloor for pumping well fluid from subsea wells to the level. The pumping assembly has a tubular outer housing that is at least partially embedded in the seafloor. A tubular primary housing locates in the outer housing and has a lower end with a receptacle. An annular space surrounds the primary housing within the outer housing for delivering fluid to a receptacle at the lower end of the primary housing. A capsule is lowered in and retrieved from the primary housing. The capsule sealingly engages the receptacle for receiving well fluid from the annular space. A submersible pump is located inside the capsule. The pump has an intake that receives well fluid and a discharge that discharges the well fluid exterior of this capsule. The capsule has a valve in its inlet that when closed prevents leakage of well fluid from the capsule. The capsule may be retrieved through open sea without a riser.