This report contains complete documentation for the 21 programs and eight data files of the EPA Continuous Flow Analyzer Automation System. This system can receive lists of samples from the Sample File Control System and return the measured concentrations to that system. It is capable of interfacing with three continuous flow analyzer detectors simultaneously. It incorporates the following major features: (1) baseline interpolation between blanks (2) multi-point calibration using first, second, or third degree regression or linear interpolation, (3) timely quality control assessments for spiked samples, duplicates, laboratory control standards, reagent blanks, and instrument check standards, (4) reagent blank subtraction, and (5) plotting of calibration curves and raw data peaks. In this document, there is a functional description, a symbol definitions table, a functional flowchart, a program listing, and a symbol cross reference table for each program. The structure of every data file is also detailed. Two related publications are titled, 'The Continuous Flow Analyzer Automation System Part I - Functional Specifications,' and 'The Continuous Flow Analyzer Automation System, Part II - User's Guide.'.