This guide documents the use and background of the ECOPATH II software system written for MS DOS computers for straightforward construction and parametrization of steady-state trophic models of aquatic ecosystems. ECOPATH II is structured around a system of linear equations initially proposed by J.J. Polovina and coworkers, and also incorporates routines from the computation of several maturity and network flow indices proposed by various theoretical ecologists, notably E.P. Odum and R.E. Ulanowicz.