The documents are arranged in two subseries: war diaries and other documents and an "index" (or register). Both subseries are arranged numerically by "microserial" number. They are further explained in the Archival Research Catalog (ARC) of the National Archives:
This first subseries consists primarily of daily operational journals (commonly referred to as war diaries) created by various naval commands, shore installations, ships and other activities throughout the Navy, as well as some Marine Corps commands. Most war diaries provided a day-to-day record of operational activities and sometimes administrative activities as well. War diaries were submitted by most units in the Navy, and most of the Marine Corps war diaries were submitted by aviation units such as fighter squadrons.
The quality of the diaries varied widely, with some providing detailed accounts, while other diaries contain only cursory information. For example, war diaries of some Naval Operating Bases (NOB) indicate what vessels were present or which vessels entered or departed the base on particular days, while others do not contain that information. Generally, higher level commands, commands that encompassed large geographic areas (such as naval districts), and large ships (such as aircraft carriers and battleships) submitted the most detailed war diaries. War diaries of smaller units and ships often provide less information.
Interspersed among the war diaries are a number of action reports submitted by various Navy ships, units and commands, providing narrative accounts of warfare operations against enemy forces as well as details of damage sustained in battle ("war damage reports"). Also interspersed among the war diaries are a number of submarine patrol reports providing details of missions undertaken by American underwater forces, as well as a number of "war histories," narrative accounts describing the activities of a particular ship, station or command during the war.
The first subseries also contains British Admiralty (naval headquarters) war diaries from the outbreak of war in Europe in September 1939 to the fall of 1945, and signals (radio communication) documentation relating to the evacuation of British and French forces from Dunkirk, France, during late May-early June 1940. There are also compiled reports on various small-scale surrenders of Japanese forces scattered around the Pacific Theater of Operations during the fall of 1945.
The second subseries consists of an "index," or register, consisting of lists indicating what documents are contained on each reel of microfilm. Information in the index includes each document's microserial number, its creator (ship, unit or command), the type of document (such as war diary, action report, or war history), the creator's filing classification and document serial number, the dates covered by the content of the document, and the date the document was created.