Partial Contents: List of figures; Introduction and general instructions (Introduction, List of indicators, Training and qualifications, Safety, Protocols, Quality control and laboratory audits); Water quality (Performance-based methodologies, Dissolved inorganic nitrogen - ammonia, Dissolved inorganic nitrogen nitrate-nitrite, Total nitrogen and phosphorus, Total phosphorus and freshwater orthophosphate, Orthophosphate (saltwater only), Chlorophyll a; Fecal indicator (Scope and application, Summary of method, Definitions of method, Interferences, Health and safety warnings, Personnel qualifications, Equipment and supplies, Reagents and standards, Preparations prior to DNA extraction and analysis, Procedures for processing and QPCR analysis of sample concentrates, Storage and timing of processing/ analysis of filter concentrates, Chain of custody, Quality control/quality assurance, Method performance, Record keeping and data management, Waste management and pollution prevention, References, Tables, diagrams, flowcharts, checklists, and validation data); Contaminants (Sample preparation for metals analysis, Sample preparation for organic compounds in fish tissue and Sediments), Polychlorinated biphenols (PCBS) in fish tissue and sediments, Polynuclear aromatic hydrocarbons (PAHs) in sediments only); Sediments (Sediment grain size and characterization, Assessing sediment toxicity using estuarine and marine amphipods, Sediment toxicity using freshwater amphipods); Infaunal benthic macroinvertebrate communities Scope and application, Summary of method, Sample storage and treatment, Sorting, Procedure, Quality assurance and quality control, References.