Aquatic Ecology

Aquatic Ecology

ESI offers comprehensive aquatic ecological services for resource inventories and regulatory compliance, including the Endangered Species Act (ESA) and Clean Water Act (CWA).  ESI’s aquatics team is a diverse group of biologists with specialties including water quality (limnology) and specific taxa, like mussels, fish, crayfish, and aquatic insects and other macroinvertebrates.  We use field techniques appropriate for the wide variety of freshwater aquatic habitats where we work, ranging from small creeks to large river systems like the Ohio, Allegheny, Mississippi, New, Delaware, and Susquehanna, among others.  Our staff is listed on many state- or drainage-specific “qualified surveyor lists,” we maintain state scientific collection permits, and we hold a federal permit from USFWS covering 30 species of listed mussels and 4 species of listed fish. 

Water Quality Assessments

Services aquatics water qualityESI assists our clients to meet their permit requirements under §404 and §401 of the Clean Water Act, including jurisdictional waters determinations and state water quality certifications. We use the USEPA’s protocols and the USACE’s permitting procedures. We utilize the Qualitative Habitat Evaluation Index (QHEI) and Headwater Habitat Evaluation Index (HHEI) as designated in the states of Ohio and Indiana as well as the Kentucky Department for Surface Mining Reclamation and Enforcement (DSMRE) Constructed Vegetation Stratum Rank System.

ESI uses state-of-the-art water quality field and laboratory equipment including YSI multiprobes, HACH spectrophotometers, and IDEXX Quanti-Tray systems.

                         Water quality parameters frequently sampled include:

  • • nutrients (nitrate, phosphorus, ammonia)
  • • bacteria (e.g., coliform,E. Coli, Streptococcus)
  • • dredge or grab sampler
  • • oversized meter surber sampler assessed by SCUBA
  • • deep water artificial substrate sampling
  • • benthic macroinvertebrate trawling

Freshwater Mussels

Services aquatics musselsESI’s professional malacologists complete mussel surveys for large and small scale projects ranging from simple habitat assessments at stream crossings to full coverage and relocation surveys associated with bridge and dam replacements.  Typical data recordation includes habitat/substrate, mussel density, species diversity, and depth for bathymetric mapping.

Members of the ESI mussel survey team are certified divers; we use SCUBA with full face mask or surface air supply, and underwater communication equipment.  Surveys in shallow water are completed with snorkel equipment. 

                         Our staff uses all standard survey methods:

  • • excavation sampling
  • • spot-dives
  • • video transects
  • • live counts


Services aquatics macroinvertebratesWe complete studies of aquatic macroinvertebrates for a variety of clients, often as a component of a water quality biomonitoring requirement.  We use a variety of methods for data collection and analysis, including indices like the US EPA’s Rapid Bioassessment Protocols (RBPs), Invertebrate Community Index (ICI), EPT Index, Hilsenhoff Index of Biotic Integrity (HBI), Shannon-Wiener Diversity Index, and Kentucky Division of Water’s Methods for Assessing Biological Integrity of Surface Waters.  Samples are sorted and identified by NABS certified taxonomists to the lowest possible taxon, typically genus.  We process all aquatic taxa, including mounting and identification of midges (chironmids).

                         Our traditional and specialized sampling gear and methods include:

  • • hardness
  • • suspended and dissolved solids
  • • biological oxygen demand / chemical oxygen demand
  • • metals (e.g., nickel, copper, lead, cadmium, chromium, zinc)
  • • organics (e.g., VOC, BCPs, pesticides, herbicides, oil and grease)
  • • cyanide and hexachrome


Services aquatics fishESI provides a breadth of services related to fish ecology and fisheries management.  We complete many types of studies for wildly disparate goals.  We complete survival studies at hydroelectric facilities, develop disturbance-monitoring plans for the mining industry, and advise on the size and configuration of culverts for fish passage on DOT projects.

We use standard collection methods and protocols including the US EPA’s Rapid Bioassessment Protocols.  We collect and identify species to calculate species richness and composition metrics for ranking of water body health.  We use EPA’s Index of Biotic Integrity (IBI) to evaluate pollution tolerance, trophic function, abundance, and fish community condition.

                        We are competent with all types of fish sampling techniques:

  • • electrofishing – backpack tote-barge and 18-foot boat
  • • Missouri modified benthic trawling methods
  • • SCUBA and/or snorkeling


Services aquatics crayfishAstacology is one of ESI’s unique professional capabilities.  We conduct surveys for aquatic, terrestrial, and cave crayfish.  Survey efforts range from desktop habitat reviews (many species are endemic to a few caves or small watersheds) to species-specific presence/absence surveys, to multi-species inventories (including detection of invasive species).  We use a variety of report and sample techniques to ascertain distribution, density, diversity, and obtain a census estimate.  Many survey methods and types of equipment are used:



  • Burrowing Species (primary/secondary burrowers)

  • • mist net traps
  • • pipe traps
  • • terrestrial funnel traps
  • • pitfall traps
  • • fiber optic scopes
  • • excavation of burrow


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