This publication contains the user's guide to the EPA Continuous Flow Analyzer Automation System. This system can receive lists of samples from the Sample File Control (SFC) System and return the measured concentrations to that system or the automation system can operate independently of SFC and only output the final results to a hardcopy unit. 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. This document contains detailed descriptions and examples of the features of the system, as they appear to the user. Two related publications are titled, 'The Continuous Flow Analyzer Automation System, Part I -- Functional Specifications,' and 'The Continuous Flow Analyzer Automation System, Part III -- Program Documentation.'.