Early in 1996, a Cray C90 was installed at GFDL with 16 processors, 256 Mwords of central memory, 1 Gword of solid state disk, and 370 Gbytes of rotating disk. Later that year, the system was replaced by a Cray T90 having 20 processors, 512 Mword central memory and a 2 Gword solid state disk. The Cray T90 was later upgraded to 26 processors in 1997 and a Cray T3E with 40 processors and 640 Mwords of memory also arrived. In 1998, a Cray T90 with 4 processors was added. In 1996, a beta version of MOM 2 (version 2) was made available as a stepping stone to MOM 3. In anticipation that parallelization will be needed to keep overall system efficiency high in the future, attention has been and continues to be placed in this direction. Throughout these developments, the intent has been to construct a flexible research tool useful for ocean and coupled air-sea modeling applications over a wide range of space and time scales. As outlined below, progress with parallelization, and the implementation of fundamentally new physics and numerics options, motivated the release of MOM 3 which is described within this manual.