Research Focus Areas
Together with our partners, the Hudson River Research Reserve identified research focus areas (RFAs) that support the resilience of the Estuary’s natural resources and communities. These focus areas are intended to inspire collaborative projects that address critical scientific questions about habitats, restoration and stewardship, and flora and fauna. Our goal is to deliver the innovative technical assistance that resource managers and communities need to meet the demands of a changing estuary over the next five years. Download a PDF overview of the Research Focus Areas.


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.

Restoration & Stewardship

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.

Research Focus Area (RFA) Library

This library identifies resources, partners and current or past research projects supported by the Hudson River Reserve for each of the research focus areas identified at the 2020 Research at the Reserve Forum. That event brought more 80 scientists together to identify research gaps and opportunities to explore over the next five years. Back to top.

RFAThemeProjects & ResearchersResourcesPartnersKeywords
Detect invasive species using eDNASpeciesWatts, NERRS eDNA; Miranda et al. 2015 American Eels eDNA Bronx RiverFisheries DataHR Fisheries, DEC Forest, SUNY ESFInvasive Species
Baseline fish biomass assessment in different river componentsSpeciesFisheries monitoringFisheries Data, Benthic Maps, HRNERR River Bottom Mapping DataHREP, HR Fisheries - NYDECFish
Migration & feeding behavior of Black drum (Pogonias cromis) & Freshwater drum (Aplodinotus grunniens) SpeciesFisheries monitoringFisheries DataHREP, HR FisheriesFish, Mollusks
Larval fish abundance & conditionSpeciesUtilities fish survey, Yong Chen SUNY Stony Brook; Chris Nack Assemblages SWMP water quality dataDEC Fisheries, Cornell, Hudson River Foundation, SUNY ESF, GreenwayFish
Use of artificial reefs by fishes, crabs, & other nektonRestorationDeGasperis, Piermont OysterPiermont Oyster reef dataHR Fisheries, DEC Marine artificial Reef programFish, Mollusks
Re-survey spotfin killifish in remnant Piermont Marsh Spartina patensSpeciesYozzo & Ottman 2003 Spotfin Killfish distributionPiermont Marsh Tidal Wetland mapsHR Fisheries, Cornell IRISFish, Piermont
Fish assemblages to assess habitats, restoration, & Phragmites impactsSpeciesGays Point restoration, DeGasperis; Nack et al. 2015Fisheries data, Habitat Mapping and Resilience, Tidal Wetland and SAV mapsHREP, HR Fisheries, Cornell IRISFish
Expand eel monitoring & related student researchSpeciesEel Project monitoring Eel Project Data, Eel Project PresentationHREP, MaristFish, Monitoring, American eel
Citizen science to identify fish using photographySpeciesFisheries Herring Monitoring Fisheries Herring dataHR FisheriesFish, Methods, Citizen science
Study migratory behavior of Tessellated darterSpeciesDuryea & Schmidt 1986, Feeding Biology at Tivoli BayFisheries data; NERR fish monitoringHR FisheriesFish, Tessellated darter
Essential access in tributaries for white sucker & Smallmouth bassSpeciesEel Project monitoring Eel Project Data, Eel Project PresentationHREPFish, White sucker, Smallmouth bass
Significance of species tributary spawning to total spawningSpeciesEel Project monitoring; Fisheries Herring Monitoring Eel Project Data, Fisheries Herring data; Eel Project PresentationHREP, HR FisheriesFish, Tributaries
Significance of Vallisneria returning; productivity & fecundity of different genotypesSpeciesPerkins & Neel 2019; Carew & Englehardt 2018Habitat MapsHREP, Cornell IRIS, HRFVegetation, Restoration
SAV habitat model for future restoration efforts at multiple sitesHabitatGays Point restoration, DeGasperisSAV maps, Habitat Mapping and Resilience, Habitat MappingHREP, Cornell IRIS, HRFSAV, Modeling, Side channel restoration
Analyze SAV maps & data for differences between east & west side of riverHabitatCarroll 2020 SAV mapsHREP, Cornell IRISSAV
Apply Sean Carroll methodology on SAV maps from 2018 dataHabitatCarroll 2020 SAV maps, SAV hurricane recovery analysisHREP, Cornell IRISSAV, Modeling
Conduct long-term biological monitoring for juvenile fish in SAVSpeciesFisheries monitoringFisheries Data; SAV mapsHR Fisheries, Cornell IRISSAV, Monitoring, Fish
Impacts of increasing upland, watershed, & shoreline erosion on sediment dynamics & tidal wetlandsHabitatDaSH projectDaSH data, SET data, LDEO sediment coresHREP, UMass, Cary, LDEOSediment, Climate Change
Link land use & lake data for past drought indicationsHabitatTBDHudson Valley Natural Resource MapperHREPSediment, Climate Change
Sediment data to see if precipitation increase is observableHabitatPederson et al. 2005Meteorological data from NERRS and Cary, UMass, LDEO and Cary Sediment coresUMass, Cary, LDEOSediment, Climate Change
Studies on sediment flux & deposition for SAV understanding HabitatDaSH team; McKeon; ChangSAV maps, SAV Volunteer Monitoring data, SSAM-1 SAV Monitoring data, TTS from SWMP dataHREP, Cornell IRIS, GreenwaySediment, SAV, Modeling, Climate Change
Final resting for sediment from Hurricane Irene & Tropical Storm LeeHabitatWall & Hoffman 2012; Ralston et al. 2013Benthic Maps; NERR/HRECOS turbidity data, River Bottom MappingHREP, USGS, Woods HoleSAV, Modeling
Sediment core data analysis gap in quality versus quantity HabitatDaSH projectLDEO sediment coresUMass, Cary, LDEOSediment
Effect of deglaciation (isostatic rebound) on wetlandsHabitatPeteet et al. 2007; Peteet 2011LDEO sediment coresLDEOAccretion
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. 2012LDEO sediment coresLDEOAccretion
Assisted accretion, dredge material thin-layer deposition RestorationFernald 2020 NSC ProjectSET dataNYNJHEPAccretion
Marsh resilience strategies: conserving locations for planned marsh migrationRestorationTabak et al. 2016; Scenic Hudson land protectionScenic Hudson SLAMM Scenic HudsonAccretion, Marsh Migration, Sea Level Rise, Climate Change
Marsh resilience strategies: enhanced nitrogen removalHabitatTBDTBDHREPEcosystem Functions and Services, Water Quality, Climate Change
Accretion rate differences in short term SET data vs long-term cores (ecomposition & compaction)HabitatDaSH Project; Ralston et al. 2021NERR SET data; LDEO sediment coresUMass, LDEO, CarySediment, Accretion, Sea Level Rise
Determine if marshes keep up with sea level & subsidence ratesHabitatOrton, Storm Surge BarriersNERR SET data; LDEO sediment coresStevens Institute, UMass, LDEO, CaryModeling, Marsh Migration, Sea Level Rise
Proposed gate storm surge barriers impacts, different closure durations, storm events, & sea level riseHabitatOrton, Storm Surge BarriersStevens Hydrologic modelStevens Institute, US Army Corps of EngineersModeling
Functional importance of southern wetlands in northern riverHabitatTBDTidal Wetland MapsCary, Hudsonia, Cornell IRISEcosystem Functions and Services
Effect of increasing nitrogen on carbon lability & decomposition in marshesHabitatTimothy Morin, SUNY ESF; Peteet et al. 2020LDEO Sediment cores, USCA Blue Carbon projectUMass, LDEO, Cary, SUNY ESFEcosystem Functions and Services, Water Quality
Best models for edge stabilization at Piermont. Examples from Jamaica Bay, ACE Basin, etc.RestorationPiermont edge stabilization project Tidal Wetland MapsScience and Resilience Institute at Jamaica BAyErosion, Piermont
Edge erosion causes at Piermont. Examples from Jamaica Bay & Long IslandHabitatPiermont edge stabilization project Tidal Wetland MapsScience and Resilience Institute at Jamaica BAyErosion, Piermont, Water Quality
Habitat impact of permanently placed protection or stabilization structuresHabitatPiermont edge stabilization project Tidal Wetland Maps, Habitat Mapping and ResilienceHREPErosion, Piermont, Monitoring
Marsh-human interface, adjacent infrastructure relationships, & marsh value to humansHabitatSheng, Marsh Value; Tabak et al. 2016SLAMM, habitat and shoreline maps, SSAM-1 SAV Monitoring data, Sheng economic tool, Habitat Mapping and ResilienceHREP, Scenic Hudson, NSC, GreenwayMarsh Migration, Ecosystem Functions and Services, Restoration, Climate Change
Resuspension or release of heavy metals (Cu, Pb, Zn) & legacy contaminants in marsh sedimentsHabitatPeller and Bopp 1985; Benoit et al 1999LDEO sediment coresHREP, UMass, LDEO, CaryContaminants
Historical maps & imagery for marsh changesHabitatMiller et al. 2006Tidal Wetland and SAV maps, Benthic Maps, River Bottom MappingHREP, Cornell IRISMarsh Migration, Sediment
Effect of land use overtime on sediment supply in wetlandsHabitatMiller et al. 2006Land use maps, Miller historic maps, Sentinal Site dataHREPMarsh Migration, Sediment
Early accretion rates in Tivoli Bays when wetlands formed in 1850sHabitatDaSH project; Kelly McKeon NSF graduate fellowship project Land use maps, Miller historic maps, UMass, LDEO, Cary sediment cores, sentinal site dataHREP, UMass, LDEO, CaryAccretion, Tivoli
Impact on rare plants (Spartina & Lilaeopsis) by the encroachment of Phragmites in Piermont MarshSpeciesDeGasperis, Piermont OysterTidal Wetland maps; Piermont vegetation data (DeGasperis)Cornell IRISVegetation, Invasive Species, Monitoring
Cause & mitigation options for grazing damage: deer, geese, crabs, other at Piermont MarshHabitatNSC Wildlife camera proposal (Raposa) - TBDTidal Wetland maps; Piermont vegetation data (DeGasperis)Cornell IRISPiermont
Management options to mitigate stresses on wetlandsRestorationSheng Piermont Marsh project Piermont Marsh storm ProtectionNYSERDAWater Quality
Spatial variation of vegetation & nutrient levels impacting ecological communitiesHabitatOsborne et al., 2015NERR nutrient data, Tidal Wetland mapsCary, Cornell IRISWater Quality
Effects of nitrogen pollution & denitrification on marshes through time; N & N15 curves & core profilesHabitatNguyen & Peteet 2010 Stable Isotope AnalysisLDEO sediment coresUMass, LDEO, CaryWater Quality, Contaminants
Full range of habitats & change, if interchange is redundant or unique, biogeochemistry relationshipHabitatTabak et al. 2016SLAMM model, Tidal Wetland Maps, Habitat Mapping and ResilienceScenic Hudson, Cornell IRISModeling, Monitoring
Causes & impacts of interior ponding at Piermont MarshHabitatHRNERR Sentinel Sites MonitoringNERR SET data, Tidal Wetland mapsCornell IRISPiermont
Long term vegetation community monitoring to evaluate biodiversity & changeHabitatHRNERR Sentinel Sites MonitoringNERR sentinel sites, Tidal Wetland mapsCornell IRISMarsh Migration, Monitoring
Collaborate to map aquatic invasive species distributionRestorationWei Fang, Pace University NERR sentinel sites, Tidal Wetland mapsLower-Hudson PRISM, mid-Hudson PRISM, NYSDEC Invasive SPecies UnitInvasive Species
Round goby monitoring with new tools, techniquesSpeciesWatts NERRS eDNAFisheries monitoringHR FisheriesInvasive Species, Fish, Monitoring
Spiny water flea impact on alewivesSpeciesHR Fisheries MonitoringFisheries monitoringHR FisheriesInvasive Species, Fish
Aquatic fauna invasive species monitoringSpeciesWei Fang NSC Trapa proposalNERR sentinel sites, Tidal Wetland mapsLower-hudson PRISM, NYSDEC Invasive SPecies UnitFish, Invasive Species, Monitoring
Freshwater mussels surveySpeciesDave Strayer 1999HREP, CaryMollusks
Upstream tributary land use & land cover impacts on flooding, stormwater runoff, & nutrient or sediment loadingHabitatTBDHudson Valley Natural Resource MapperHREPSediment, Water Quality
Nitrogen sources & mitigation solutionsHabitatTBDNERR nutrient dataSparkill Creek Watershed AllianceWater Quality, Piermont
Tide changes with Turkey Point tide gauge stationRestorationSentinel Sites MonitoringTurkey Point water level stationNOAAWater Level, Sea Level Rise, Climate Change