Research Focus Areas

Our Research Focus Areas provide context for the many research questions that we and our partners aim to pursue, centering these questions around important themes for the resilience of the Estuary’s natural resources and communities. They are intended to inspire collaboration among researchers with similar interests and priorities. Click here to download a PDF overview of the Research Focus Areas.

To learn more about the specific research questions that fall within each focus area, check out our Library of Research Questions below.


As the Hudson’s habitats change, scientists have prioritized exploring the presence, abundance, and behavior of fauna and flora through innovative methods, including eDNA and citizen science. They also want to study faunal assemblages and behavior to understand the impacts of changing habitats on different life stages. Back to top.

Research DRIVERS

Non-native plants, fish, and invertebrates are altering the biodiversity and ecological functions of Hudson River habitats, leading to the loss of native species, ecological shifts, and changes in recreational use of the Estuary. Introduction of new non-natives continues, and where these are invasive, they compound the problems.

Collaborative Science

The Hudson River Research Reserve works with partners to facilitate fish and invertebrate research across a range of habitats and advance innovative methods for species identification.

  • The American Shad Assemblage Study at our Stockport Flats site identified the area as key nursery habitat for shad and an important refuge for other fish and vegetation during large storms like Hurricane Irene and Tropical Storm Lee.
  • At our Iona Island and Piermont Marsh sites, fish ecology studies have explored patterns of nekton habitat utilization in Phragmites australis and Typha angustifolia marshes, developed new distribution records for the spotfin killifish, and compared invertebrate communities between marsh types.

Learn more about flora and fauna-related research focus areas (RFAs) and related resources in the RFA library.


To support natural resource protection in these changing conditions, scientists want to explore the effects of accretion, erosion, and sea level rise on marsh resilience; test innovative approaches to wetland restoration; study species interactions in restoration sites; and model edge stabilization to further adaptive management. Back to top.

Research DRIVERS

Sea levels have been rising at a rate of 2.87 mm per year at New York Harbor’s Battery tide station, and spatial models project the Hudson’s wetlands to change significantly over the next century. More powerful storms, heavier rainfall, and larger storm surge will flood coastal communities, compact marsh surfaces, and shift sediment flows and deposits in wetlands. 

Research & Training

Our research, training, and monitoring programs collaborate to support habitat restoration and stewardship throughout the Hudson River Valley.

  • The Hudson River Sustainable Shorelines Project provides science-based recommendations, case studies, and data for shore zone management that enhances natural benefits while meeting protection needs.
  • The 2016 Climate Change Resilience Webinar synthesized information about Hudson River tidal wetland migration pathways and Hudson Valley conservation strategies.
  • The Piermont Marsh Storm Protection Study (2016–2020) explored how marshes protect the Village from storm-driven flood and waves.
  • The Submerged Aquatic Vegetation  Restoration Workshop faciliated knowledge sharing on the feasibility of restoring Vallisneria americana after a historic loss during 2011 storms.

Search restoration and stewardship related focus areas (RFA) and related resources in the RFA library.


The region’s scientists want to map the composition and distribution of submerged aquatic vegetation, tidal marshes, shallows, shorelines, and benthic communities; develop protocols to measure changes in cover, elevation, and plant productivity; and assess the ecological functions of Hudson River habitats, including their potential for blue carbon sequestration Back to top.

Research DRIVERS

Multiple consequences of climate change are predicted to impact the Hudson River’s globally unique freshwater tidal habitats. Where wetland elevations fail to keep pace with rising waters, these habitats will migrate or disappear. However, if properly managed, they could continue to provide significant benefits, including storm protection, water quality improvement, and carbon sequestration.

Mapping & Monitoring

Our monitoring program tracks habitats as they respond to changes in sea levels, sediment dynamics, and nutrient loads. This high quality baseline data provides a platform for us to collaborate with partners on research that meets the needs of natural resource managers. 

  • Collaborative mapping efforts have helped characterize critical changes in the region. Multiple habitat mapping projects are ongoing, characterizing shallow and benthic habitats, submerged aquatic vegetation, and tidal wetlands.
  • Monitoring at our Tivoli Bays site evaluates the ecological impacts of sea level changes and increased storm surge on submerged aquatic vegetation and emergent tidal marsh habitats.

Search habitat research focus areas (RFA) and related resourcs in the RFA library.


The region’s scientists understand the critical importance of examining the interaction of people with our ecosystems. They aim to invite diverse voices and perspectives to guide research, breaking barriers to community involvement. Back to top.

Research DRIVERS

This research focus area represents our interest in involving people and community voices in ecological research, and in exploring the intersections between social science and conservation. We recognize that we have much to learn about the perspectives of the diverse communities along the Hudson and are actively seeking out new partnerships to pursue this.

Library of Research Questions

The searchable library below shows the specific research questions that fall within each research focus area. Some of these questions are being studied, but others are still ideas that should be pursued when resources allow. The library shows which partners are working on and/or interested in pursuing a particular topic. We intend this library to help foster collaborative research by connecting scientists with similar priorities to one another and to potential funding opportunities.

These research questions were generated following our 2020 Research at the Reserve Forum, where over 80 scientists identified research gaps and opportunities to explore over the next five yearsBack to top.

Research QuestionResearch Focus AreaProjects & ResearchersResourcesPartnersKeywords
Detect invasive species using eDNASpeciesWatts, NERRS eDNA; Miranda et al. 2015 American Eels eDNA Bronx RiverFisheries Data HR Fisheries, DEC Forest, SUNY ESFInvasive Species
Assess baseline fish biomass in different river habitatsSpeciesFisheries monitoringFisheries Data, HRNERR River Bottom Mapping Data HREP, HR Fisheries - NYDECFish
Research migration & feeding behavior of Black drum (Pogonias cromis) & Freshwater drum (Aplodinotus grunniens) SpeciesFisheries monitoringFisheries DataHR FisheriesFish, Mollusks
Assess existing larval fish abundance data and determine population status, and prioritize future data collectionSpeciesUtilities fish survey; Hudson River Biological Monitoring Program; Chris Nack Assemblages; Niemen et al. 2021 Centralized Data Management OfficeDEC Fisheries, Cornell, Hudson River Foundation, SUNY ESF, Greenway, Yong Chen SUNY Stony BrookFish, Water Quality Monitoring
Assess value of artificial reefs and other habitat enhancement projects for fishes, crabs, oysters & other nektonRestorationDeGasperis, Piermont OysterPiermont Oyster Habitat DataHR Fisheries, NYSDEC Artificial Reef ProgramFish, Mollusks
Re-survey spotfin killifish in remnant Piermont Marsh Spartina patensSpeciesYozzo & Ottman 2003 Spotfin Killfish distributionHudson River Estuary Tidal Wetlands 2007HR Fisheries, Cornell IRISFish, Piermont
Assess fish habitats and how they are impacted by restorationSpeciesGays Point restoration, DeGasperis; Nack et al. 2015Fisheries data, Habitat Mapping and Resilience, Hudson River Estuary Tidal Wetlands 2007, SAV maps HREP, HR Fisheries, Cornell IRISFish
Expand eel monitoring & related student research, in part by increasing collaboration with students and other partnersSpeciesEel Project monitoring ; Brinzac 2020Eel Project Data, Eel Project Presentation HREP, MaristFish, Monitoring, American eel
Develop a community science project to identify fish using photographySpeciesFisheries Herring Monitoring Fisheries Herring Monitoring HR FisheriesFish, Methods, Citizen science
Study migratory behavior of Tessellated darterSpeciesDuryea & Schmidt 1986, Feeding Biology at Tivoli Bay; P. Miller 2015 (thesis)Fisheries data; NERR fish monitoringHR FisheriesFish, Tessellated darter
Identify tributaries that are essential for white sucker & Smallmouth bassSpeciesEel Project monitoring ; P. Miller 2015 (thesis)Eel Project Data, Eel Project Presentation HREPFish, White sucker, Smallmouth bass
Determine the significance of particular tributary spawning areas to overall species successSpeciesEel Project monitoring; Fisheries Herring Monitoring; Kowalik 2018 (thesis); Kowalik and Eakin 2019Eel Project Data, Fisheries Herring data; Eel Project Presentation HREP, HR FisheriesFish, Tributaries
Determine the significance of different genotypes of Vallisneria for the resilience of the species in different zones of the HudsonSpeciesPerkins & Neel 2019; Carew & Englehardt 2018; Carew 2019 (thesis)Hudson River Estuary Documented Submerged Aquatic Vegetation HREP, Cornell IRIS, Hudson River FoundationVegetation, Restoration
Determine priority locations on the Hudson for SAV restoration and develop methodology for restorationHabitatGays Point restoration, DeGasperis; Hamberg 2015 (thesis)SAV maps, Habitat Mapping and Resilience, Habitat Mapping HREP, Cornell IRIS, Hudson River FoundationSAV, Modeling, Side channel restoration
Analyze SAV maps & data for variation based on locational characteristics and river dynamics HabitatCarroll 2020 SAV maps, SAV hurricane recovery analysis HREP, Cornell IRISSAV, Modeling
Conduct long-term biological monitoring for juvenile fish in SAVSpeciesFisheries monitoringFisheries Data; SAV mapsHR Fisheries, Cornell IRISSAV, Monitoring, Fish
Assess the impacts of increasing upland, watershed, & shoreline erosion on sediment dynamics & tidal wetlandsHabitatDaSH project; Yellen et al. 2021; Ralston et al. 2021DaSH data, SET data, LDEO sediment cores HREP, UMass, Lamont Doherty, Cary IESSediment, Climate Change
Link land use & lake data for past drought indicationsHabitatTBDHudson Valley Resource Mapper HREPSediment, Climate Change
Assess historic sediment cores to analyze precipitation trends, particularly as the climate changesHabitatPederson et al. 2005Meterological data from NERRS, UMass, LDEO sediment cores and Cary IES Sediment coresUMass, Lamont Doherty, Cary IESSediment, Climate Change
Assess the impacts of sediment flux and deposition on aquatic vegetation over timeHabitatDaSH team, McKeon 2021 (thesis), Clara ChangSAV maps, SAV Volunteer Monitoring data, SSAM-1 SAV Monitoring data, TTS from SWMP data HREP, Cornell IRIS, GreenwaySediment, SAV, Modeling, Climate Change
Model sediment movement after storm events such as Hurricane Irene and Tropical Storm Lee, and assess the implicationsHabitatWall & Hoffman 2012; Ralston et al. 2013NERR/HRECOS turbidity data, River bottom maps HREP, USGS, Woods HoleSAV, Modeling
Sediment core data analysis gap in quality versus quantity. HabitatDaSH projectLDEO sediment coresUMass, Lamont Doherty, Cary IES, Matt Reid, CornellSediment
Determine the effect of deglaciation (isostatic rebound) on wetlandsHabitatPeteet et al. 2007; Peteet 2011LDEO sediment coresLamont DohertyAccretion
Determine accretion rates through time via marsh core & accelerator mass spectrometry (AMS) macrofossil dating HabitatPeteet et al. 2007; Peteet 2011; Chou and Peteet 2009; Sritairat et al. 2012; Peteet et al. 2020LDEO sediment coresLamont DohertyAccretion
Determine the potential for thin-layer deposition in areas where assisted accretion is neededRestorationFernald 2020 NSC ProjectSET dataNYNJHEPAccretion
Prioritize locations for planned marsh migrationRestorationTabak et al. 2016; Scenic Hudson land protectionProtecting the PathwaysScenic HudsonAccretion, Marsh Migration, Sea Level Rise, Climate Change
Assess the potential for enhanced nitrogen removal in marshesHabitatTBDTBD HREPEcosystem Functions and Services, Water Quality, Climate Change
Compare accretion rates in short term SET data vs long-term cores (composition & compaction)HabitatDaSH project; Ralston et al. 2021; McKeon 2021 (thesis)NERR SET data; LDEO sediment coresUMass, Lamont Doherty, Cary IESSediment, Accretion, Sea Level Rise
Determine if marsh accretion rates will allow for the preservation of marsh ecosystem functions, despite sea level rise & subsidence ratesHabitatOrton, Storm Surge BarriersNERR SET data; LDEO sediment cores Stevens Institute, UMass, Lamont Doherty, Cary IESModeling, Marsh Migration, Sea Level Rise
Model the impacts of proposed gate storm surge barriers, different closure durations, storm events, & sea level riseHabitatOrton, Storm Surge Barriers; Chen et al. 2020Assessing the Effects of Storm Surge Barriers on the Hudson River Estuary Stevens Institute, US Army Corps of EngineersModeling
Study the functional importance of southern wetlands in northern riverHabitatFindlay et al. 2019Hudson River Estuary Tidal Wetlands 2007Cary IES, Hudsonia, Cornell IRISEcosystem Functions and Services
Determine the effect of increasing nitrogen on marsh respiration, specifically carbon lability & decompositionHabitatTimothy Morin, SUNY ESF; Peteet et al. 2020LDEO sediment cores, USCA Blue Carbon projectUMass, Lamont Doherty, Cary IES, SUNY ESF, Matt Reid, CornellEcosystem Functions and Services, Water Quality
Determine the causes of erosion and the best models for edge stabilization at Piermont Marsh, using examples from Jamaica Bay, Long Island, ACE Basin, etc.Restoration, HabitatPiermont edge stabilization project Hudson River Estuary Tidal Wetlands 2007Science and Resilience Institute at Jamaica BayErosion, Piermont, Water Quality
Determine the impacts of permanently placed protection or stabilization structures on habitatHabitatPiermont edge stabilization project Hudson River Estuary Tidal Wetlands 2007, Habitat Mapping and Resilience HREPErosion, Piermont, Monitoring
Determine marsh value to humans by studying areas where marshland and human land uses (particularly human infrastructure) convergeHabitat, PeopleSheng, Marsh Value; Tabak et al. 2016Protecting the Pathways, habitat and shoreline maps, SSAM-1 SAV Monitoring data, Sheng economic tool, Habitat Mapping and Resilience HREP, Scenic Hudson, NSC, GreenwayMarsh Migration, Ecosystem Functions and Services, Restoration, Climate Change
Analyze the resuspension or release of heavy metals (Cu, Pb, Zn) & legacy contaminants in marsh sedimentsHabitatPeller and Bopp 1985; Benoit et al 1999LDEO sediment cores HREP, UMass, Lamont Doherty, Cary IESContaminants
Use historical maps & imagery to analyze marsh changesHabitatMiller et al. 2006, Lau & Yellen 2021Hudson River Estuary Tidal Wetlands 2007, Hudson River Estuary Documented Submerged Aquatic Vegetation, River bottom maps HREP, Cornell IRISMarsh Migration, Sediment
Determine the effect of land use over time on sediment supply in wetlandsHabitatMiller et al. 2006, DaSH projectLand use maps, Miller historic maps, Sentinal Site data HREP, McKeon et al. 2022Marsh Migration, Sediment
Use our understanding of early accretion rates in Tivoli Bays (when wetlands formed in 1850s) to inform the creation of human-made intertidal marshes on the HudsonHabitatDaSH project, Kelly McKeon NSF graduate fellowship project Land use maps, Miller historic maps, UMass, LDEO, Cary sediment cores, sentinal site data HREP, UMass, Lamont Doherty, Cary IESAccretion, Tivoli
Impact of nonnative Phragmites encroachment on rare plants (Spartina & Lilaeopsis) in Piermont MarshSpeciesDeGasperis, Piermont OysterHudson River Estuary Tidal Wetlands 2007; Piermont vegetation data (DeGasperis)Cornell IRISVegetation, Invasive Species, Monitoring
Determine the species responsible for herbivory at Piermont Marsh, and develop options for mitigationHabitatNSC Wildlife camera proposal (Raposa) - TBDHudson River Estuary Tidal Wetlands 2007; Piermont vegetation data (DeGasperis)Cornell IRISPiermont
Identify stressors on marshes, particularly Piermont Marsh, and determine options for preserving ecosystem structure and services RestorationSheng Piermont Marsh project Piermont Marsh storm protection studyNYSERDAWater Quality
Develop a model to determine whether and how nutrient levels impact spatial variation of vegetationHabitatOsborne et al., 2015NERR nutrient data, Hudson River Estuary Tidal Wetlands 2007, SAV mapsCary IES, Cornell IRISWater Quality
Study the effects of nitrogen pollution & denitrification on marshes through time (using N & N15 curves & core profiles)HabitatNguyen & Peteet 2010 Stable Isotope AnalysisLDEO sediment coresUMass, Lamont Doherty, Cary IESWater Quality, Contaminants
Full range of habitats & change, if interchange is redundant or unique, biogeochemistry relationshipHabitatTabak et al. 2016Protecting the Pathways, Hudson River Estuary Tidal Wetlands 2007, Habitat Mapping and ResilienceScenic Hudson, Cornell IRISModeling, Monitoring
Determine the causes & impacts of interior ponding at Piermont MarshHabitatHRNERR Sentinel Sites Monitoring, Courtney et al. 2020NERR SET data, Hudson River Estuary Tidal Wetlands 2007Cornell IRISPiermont
Conduct long-term vegetation community monitoring in wetlands to determine biodiversity trendsHabitatHRNERR Sentinel Sites MonitoringNERR sentinel sites, Hudson River Estuary Tidal Wetlands 2007Cornell IRISMarsh Migration, Monitoring
Collaborate to map aquatic invasive species distributionRestorationWei Fang, Pace University NERR sentinel sites, Hudson River Estuary Tidal Wetlands 2007Lower Hudson PRISM, NYSDEC Invasive Species UnitInvasive Species
Monitor Round goby using the best available technology SpeciesWatts NERRS eDNA, George et al. 2021Fisheries monitoringHR FisheriesInvasive Species, Fish, Monitoring
Determine the impact of spiny water flea on alewivesSpeciesHR Fisheries MonitoringFisheries monitoringHR FisheriesInvasive Species, Fish
Monitor aquatic fauna in areas dominated by aquatic invasive speciesSpeciesWei Fang NSC Trapa proposalNERR sentinel sites, Hudson River Estuary Tidal Wetlands 2007Lower Hudson PRISM, NYSDEC Invasive Species UnitFish, Invasive Species, Monitoring
Survey freshwater mussels and research the need and/or feasibility of restocking or relocating freshwater mussels to restore populations in areas of decline or extirpationSpeciesDave Strayer 1999Hudson River Natural Resources Damage Unit- Mussel Reports HREP, Draft HREP Agenda,Cary IES, Mayer et al. 2020Mollusks, Freshwater mussels, Oysters, Bivalves
Research the impacts of upstream tributary land use to better understand stressors such as source pollutants, sediment, nutrient, and land cover impacts on flooding, stormwater runoff, and nutrient & sediment loadingRestoration/HabitatMcKeon et al. 2022Hudson Valley Natural Resource Mapper, Dams and Sediment in the Hudson (DaSH) HREP, Draft HREP AgendaSediment, Water Quality
Identify nitrogen sources & determine mitigative solutions to minimize nitrogen inputHabitatTBDNERR nutrient data Sparkill Creek Watershed AllianceWater Quality, Piermont
Use real-time data from the Turkey Point tide gauge station to compare existing sea level rise projections with observed sea level riseRestorationSentinel Sites MonitoringTurkey Point water level station
NCRR Part 490- Projected Sea-level Rise
NOAAWater Level, Sea Level Rise, Climate Change
Create healthy watershed model to Identify Healthy Streams and Rivers for priority protection. Include scenery and community valueHabitat/People Rotating Intensive Basin Studies (RIBS)Draft HREP Agenda, NYSDEC Division of Waterbiological monitoring, healthy watershed, protection, model
Research the risks associated with microplastics to fish and tidal water aquatic life in the Hudson Estuary, through a consideration of plastics in the water column, aquatic habitats and biological communitiesHabitat Micro-Plastics in the Hudson, Polanco et al. 2020Draft HREP Agendaplastic, micro plastic
Evaluate ambient water quality in Environmental Justice (EJ) and disadvantaged communities to determine if there are trends in non-EJ vs EJ and if EJ communities are at high risk of contaminated drinking water People EPA's Environmental Justice Screening and Mapping Tool, Environmental Justice Mapping Tools for NYS CommunitiesDraft HREP AgendaEJ, Environmental Justice, community, water quality trends
Monitor pre and post dam removal conditions to evaluate project effectiveness. Restoration Strooks Felt Dam and Furnace Brook removals Furnace Brook eDNA in Estuaries, Dams and Sediment in the Hudson (DaSH)Draft HREP Agendafurnace brook, eDNA
Develop a multi-objective optimization tool for stream barrier removal (e.g. minimize; cost, social barriers, natural barriers and maximize river miles) Restoration/PeopleDraft HREP Agendabarriers, river miles
Develop surveys and focus groups to characterize people perceptions of dams, impoundments and dam removal in the Estuary. Evaluate public knowledge, information sources and possible communications for positive message on dam removalPeopleDraft HREP Agendadam removal, barriers, fish passage
Evaluate vulnerabilities and risks from dam failures to downstream disadvantaged and environmental justice communitiesRestoration/People Dam Safety Preparedness, Dam Safety NY, NYSDEC Dam SafetyDraft HREP AgendaEJ, Environmental Justice, community, Dam Safety
Develop further research into partner motivations to participate in trees for tribs to maximize conservation benefitPeople Armstrong et al. 2013Draft HREP Agendatrees for tribs, motivations
Assess impacts of future transportation systems ( e.g. driverless cars, rail elevation, high speed rail) on urban waterfront environment)Restoration/PeopleDraft HREP Agendadriverless cars, high speed rail, urban water front
Develop strategies to engage stakeholders around difficult conversations about adapting homes and communities People Enhanced Engagement and Risk Communication for Underserved Communities, Risk CommunicationDraft HREP Agendarisk communication, resilience planning
Determine whether natural and nature-based climate adaptation solutions are more cost effective and resilient in the long term. Improve valuation of ecosystem services in cost-benefit analysis of adaption strategiesRestorationHudson River Sustainable Shorelines Project, A Comparative Cost Analysis of Ten Shore Protection Approaches at Three Sites under Two Sea Level Rise Scenarios, Economic Tradeoffs Between Shoreline TreatmentsHudson River Sustainable Shorelines Project: Monitoring and Lessons Learned, Statewide Shoreline Monitoring FrameworkDraft HREP AgendaMonitoring, nature based, sustainable
Build and apply tools needed to assess education programs effect on participant knowledge, intent, behavior change, and future choices. Evaluate continued engagement in programs through multiple ages and grades.PeopleDraft HREP Agenda
Evaluate how field experiences improve classroom learning, and change student attitudes and behavior towards the environment. People Draft HREP Agendaclassroom, field experience, appreciation of the Hudson River.
Research how effectively partners are communicating core messages and successfully reaching communities of color, low-income families, or member of the LGBTQ+ community. To be able improve this outreach. People Margaret A. Davidson Fellowship
Develop an economic cost/benefit analysis to identify the point of diminishing returns of increasing structural height for coastal protection RestorationMargaret A. Davidson Fellowship
Research connections between impoundments and their role in plant and animal species movement and occupation (carp, snakehead, water chestnut, phragmites)Restoration/SpeciesDraft HREP AgendaWater Chestnut, Phragmites, Knotweed, Carp, Snakehead, Impoundment, Dam, Invasive
Develop Pollutant Transport and Dispersal Models using water quality monitoring to manage community managed intakes. Habitat/PeopleHRECOS, NERRS Centralized Data Management Office (CDMO)Draft HREP AgendaIntakes, Water Supply, Model, Pollutant Transport