The purpose of this manual is to provide a framework for the assessment of ecosystem health that may be adapted, or used in whole or part for application to other regions. Methods are provided for all aspects from sampling design to laboratory analysis in great detail. The manual is divided into two sections, stressors and bioindicators, which are broken down into target components, with each component further broken down into sub-sections, as follows: Introduction: familiarizes the reader with the component or species, its background or ecological significance in the localized ecosystem, and why it was chosen as an indicator. Sampling Design: describes how sampling was conducted for each component including numbers of samples collected, seasons sampled, and site selection. Metrics: provides a brief overview of each protocol used when collecting samples, with references and links to more specific methodology. Methods: describes specific protocols for collecting, processing, and ingredients and formulas which are specific to species/sample and equipment. Minor modifications may be necessary when adapting methods to specific needs. An appendix with field data sheets and photographs that illustrate crab shell lesions is also included.