Munk was elected to the National Academy of Sciences in 1956 and to the Royal Society of London in 1976. He has been a Guggenheim Fellow three times. In 1965 he received the Arthur L. Day Medal from the Geological Society of America and in 1966 received the Sverdrup Gold Medal of the American Meteorological Society. He received the Gold Medal of the Royal Astronomical Society of London in 1968.
In 1976, he received the first Maurice Ewing Medal from the American Geophysical Union and the U.S. Navy. In 1977 he received the Alexander Agassiz Gold Medal of the National Academy of Sciences. In 1978 he was honored with the Captain Robert Dexter Conrad Award from the U.S. Navy.
In 1983 Munk was honored with the President’s National Medal of Science, the nation’s highest award for lifetime achievement in scientific research, “for his unique contributions to the sciences of the geophysics and physical oceanography which have led to a better understanding of the earth's rotation, the complexities of ocean waves, tidal processes and acoustic propagation."
In 1989 Munk was honored with the William Bowie Medal of the American Geophysical Union. In 1993 he received the Vetlesen Prize from Columbia University and the first Walter Munk Award for Distinguished Research in Oceanography Related to Sound and the Sea granted by the United States Navy and The Oceanography Society.
In 1999 Munk was awarded the Kyoto Prize in Basic Sciences for his fundamental contributions to the field of oceanography, the first time the prize was awarded to an oceanographer. In 2001, he was the inaugural recipient of the Prince Albert I Medal in the physical sciences of the oceans, which Prince Rainier of Monaco created in cooperation with the International Association for the Physical Sciences of the Oceans.
Munk was honored with the 2010 Crafoord Prize in Geosciences from the Royal Swedish Academy of Sciences for his pioneering and fundamental contributions to our understanding of ocean circulation, tides and waves, and their role in the Earth's dynamics.
Munk is a member or fellow of more than a dozen professional societies. He has served on many university, national, and international committees. Since 1968 he has been a member of JASON, a prestigious panel of military advisors. He has written more than 200 scientific papers.