Abstract: A barrier fluid seal assembly is provided for a reciprocating rod, where the reciprocation of the rod is used to pump barrier fluid through a barrier fluid chamber. The rod has first and second seals, and the barrier fluid chamber is located between the seals. Barrier fluid pressure is maintained higher than process fluid pressure so that if there is leakage past the seals, then it is barrier fluid that leaks, which keeps the seals clean and flushed. A reciprocating pump may incorporate the barrier fluid seal assembly for sealing around a plunger. A method of operating first and second reciprocating pumping cylinders provides bumpless transfer of pumping from one pumping cylinder to the other pumping cylinder. Motion controls, such as a controller using a position transducer for a hydraulic piston and a servo-valve for providing hydraulic fluid to the hydraulic piston, are used to compress liquid process fluid in one pumping cylinder prior to beginning its pumping stroke.