Since April 1989, a FORTRAN computer program has been used to compute transit losses for transmountain return flows (TRF's) in Fountain Creek. The transit-loss accounting program, which was developed as a result of a study completed in 1987 and is described in a previous report, enables daily accounting of (1) the TRF's, (2) the transit losses for the TRF's, and (3) the native streamflow (NSF) (nontransmountain water) in Fountain Creek between the City of Colorado Springs (CCS) and the Arkansas River. After 1989, a number of changes were made to the accounting program; however, the program and the changes never have been documented completely. To document the accounting program, a study was done by the U.S. Geological Survey, in cooperation with the City of Colorado Springs, Department of Public Utilities, and the Southeastern Colorado Water Conservancy District (SECWCD) to document the program changes and the use of the Fountain Creek transit-loss accounting program. Specifically, this report (1) describes the computational steps and procedures of the accounting program; (2) describes the changes that were made to the program in 1991-92 and in 1994-95; (3) provides a user manual; and (4) documents the procedures for maintaining the accounting program, the auxiliary programs, and the numerous output files.