A protocol and methods for monitoring the major physical, chemical, and biological components of stream ecosystems are presented. The monitoring protocol is organized into four stages. At stage 1 information is obtained on a basic set of parameters that describe stream ecosystems. Each following stage builds upon stage 1 by increasing the number of parameters and the detail and frequency of the measurements. Stage 4 supplements analyses of stream biotic structure with measurements of stream function: carbon and nutrient processes. Standard methods are presented that were selected or modified through extensive field application for use in remote settings.