The Hubbard Brook Ecosystem Study (HBES), begun in 1963, is an on-going, longterm effort to understand the structure and function of forest watersheds and associated aquatic ecosystems at the Hubbard Brook Experimental Forest in New Hampshire. Chemical analyses of streamwater and precipitation collections began in 1963, and analyses of lakewater collections began in 1967. This publication documents these collection methods, sites, and analytical techniques, providing a complete record to ensure the integrity of HBES data. The evolution of the HBES chemical data management system and the development of quality assurance procedures are described, as is the general algorithm by which ecosystem chemical inputs and outputs are calculated. These data represent a unique and important contribution to ecosystem science and provide an internationally recognized benchmark for assessing ecological changes.