Ecosystem Research Resources

Table 1. Resources from four EPA projects (see Ecosystem Examples) that informed the design of the Organon. This tabulation allows users to: 1) review example resources from a particular ecosystem of interest, for every step; or 2) compare resources found across different systems, for the same step. To jump to a section of interest, click: Coral Reef, Cold Water Fish, Stream, or Salt Marsh. For more about the origins, partner applications, and potential future uses of the Organon, see West et al. (2025)

Ecosystem Example	Organon Step	Linked Concept	Reference/Description
Coral Reef	1	Guam Coral Reef Initiative	Guam Coral Reef Initiative
Coral Reef	1, 2, 3, 4, 7	Restoration Guide	A Manager's Guide to Coral Reef Restoration Planning and Design (NOAA)
Coral Reef	1, 2, 3, 4, 5, 6	Action plan	Guam Coral Reef Restoration Action Plan
Coral Reef	1	SMART goals	SMART goals guidance (University of California)
Coral Reef	1	Goals	Guam Coral Reef Restoration Action Plan
Coral Reef	5	SMART objectives	SMART goals guidance (University of California)
Cold Water Fish	1	Columbia River Cold Water Refuges Plan	Columbia River Cold Water Refuges Plan (U.S. EPA)
Cold Water Fish	1	Oregon's temperature quality standards	Department of Environmental Quality : Water Temperature Standard : Water Quality : State of Oregon
Cold Water Fish	2	Table 1 citation (U.S. EPA 2003)	U.S. EPA Region 10 Guidance For Pacific Northwest State and Tribal Temperature Water Quality Standard
Cold Water Fish	2	Table 1 citation (McCullough 1999)	Review and Synthesis of Effects of Alterations to the Water Temperature Regime on Freshwater Life Stages of Salmonids, with Special Reference to Chinook Salmon
Cold Water Fish	2	Table 1 citation (Richter and Kolmes 2005)	Maximum Temperature Limits for Chinook, Coho, and Chum Salmon, and Steelhead Trout in the Pacific Northwest
Cold Water Fish	2	Historic river temperatures	Water temperature estimates of the Columbia River and tributaries in 2040 and 2080 (U.S. EPA Region 10)
Cold Water Fish	2	Value of CWR	Screening Approach to Identify the 23 Tributaries that Currently Provide CWR in the Lower Columbia River (U.S. EPA Region 10)
Cold Water Fish	3	Columbia River Cold Water Refuges Plan	Columbia River Cold Water Refuges Plan (U.S. EPA)
Cold Water Fish	3	Volume	Volume of Cold Water Refuge Associated with the 23 Tributaries Providing CWR in the Lower Columbia River and Selection of the 12 Primary CWR (U.S. EPA Region 10)
Cold Water Fish	3	Temperature	Evaluation of the potential cold water refugia created by tributaries within the Lower/Middle Columbia River based on NorWeST temperature model
Cold Water Fish	3	Future impairment	Technical memorandum for CWR report (U.S. EPA Region 10)
Cold Water Fish	4	Watershed analyses	Watershed Snapshot Assumptions and Approaches (U.S. EPA Region 10)
Cold Water Fish	5	Columbia River Cold Water Refuges Plan	Columbia River Cold Water Refuges Plan (U.S. EPA)
Cold Water Fish	5	SMART objectives	SMART goals guidance (University of California)
Cold Water Fish	5	Snapshot	Protect and Restore Snapshot Assumptions and Approaches (U.S. EPA Region 10)
Cold Water Fish	6	Regulatory intervention	Oregon fishing eRegulations website, Columbia River Zone
Cold Water Fish	6	Monitoring	Lower Columbia River Ecosystem Monitoring Program, Annual Report for Year 13
Cold Water Fish	7	Monitored	Columbia River Salmon Fishery Management Policy (Washington Fish and Wildlife Commission)
Stream	1	Regional Monitoring Networks (U.S. EPA 2016)	Regional Monitoring Networks (RMN) to Detect Changing Baselines in Freshwater Wadeable Streams
Stream	1	EPA Level III ecoregions	Ecoregions
Stream	2	Sensor data (U.S. EPA 2014)	Best Practices For Continuous Monitoring of Temperature and Flow In Wadeable Streams
Stream	4	EPA Healthy Watersheds Program	Healthy Watersheds Protection (U.S. EPA)
Stream	5	Protocol documents	RMN monitoring protocol documents
Stream	5	Stream RMN report (U.S. EPA 2016)	Regional Monitoring Networks (RMN) to Detect Changing Baselines in Freshwater Wadeable Streams
Salt Marsh	1	Ninigret Pond Salt Marsh Restoration and Enhancement Project	Ninigret Pond Salt Marsh Restoration and Enhancement Project website (RI Coastal Resources Management Council)
Salt Marsh	1	Partners	Improving Salt Marsh and Community Resilience Using Dredged Materials in Ninigret Pond
Salt Marsh	1	Ecological and social goals (Raposa et al. 2022)	Laying it on thick: Ecosystem effects of sediment placement on a microtidal Rhode Island salt marsh
Salt Marsh	1	Adaptation Strategy (Wigand et al. 2017)	Adaptation strategy for management of coastal marsh systems
Salt Marsh	2	Sea Level Affecting Marshes Model	NOAA Digital Coast website for downloading the Sea Level Affecting Marshes Model (SLAMM)
Salt Marsh	3	High marsh loss (Watson et al. 2017)	Wetland loss patterns and inundation-productivity relationships prognosticate widespread salt for southern New England
Salt Marsh	4	Targeted dredged sediment placement (Raposa et al. 2022	Laying it on thick: Ecosystem effects of sediment placement on a microtidal Rhode Island salt marsh
Salt Marsh	5	Action plan (Raposa et al. 2022)	Laying it on thick: Ecosystem effects of sediment placement on a microtidal Rhode Island salt marsh
Salt Marsh	5	Plan integration	Ninigret Pond Salt Marsh Restoration and Enhancement Project website (RI Coastal Resources Management Council)
Salt Marsh	5	Engineering consultant	Ninigret Pond Breachway Dredging and Salt Marsh Restoration (Fuss & O'Neill)
Salt Marsh	6	Monitoring plan (Raposa et al. 2022)	Laying it on thick: Ecosystem effects of sediment placement on a microtidal Rhode Island salt marsh
Salt Marsh	7	Adaptive management (Perry et al. 2020)	Implementing adaptive management into an adaptation strategy for a drowning New England salt marsh