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Complex Groundwater sites


Complex groundwater sites present significant technical challenges in achieving cleanup goals within a reasonable timeframe due to the nature and extent of contamination, geologic setting (e.g., fractured bedrock or low permeability formations), stringent cleanup goals, and lack of effective remedial options. Remedial Project Managers (RPMs) apply appropriate adaptive site management strategies and risk management approaches for addressing these complex groundwater sites.

Jump to Resources to access Policies & Guidance, Publications, Related Sites, and Tools



Complex groundwater sites carry high levels of uncertainty in achieving Response Complete (RC). Challenges may result from the site setting, nature and extent of contamination, technology limitations, or other non-technical challenges from evolving regulations, political interest, and/or public visibility. Specific examples of challenging site conditions include large-scale or deep plumes, complex geology or hydrogeology (e.g., fractured rock or low permeability formations including matrix diffusion), certain types of contamination (e.g., dense non-aqueous phase liquid [DNAPL] source zones), and adverse geochemical conditions.

A comprehensive risk-based approach can be protective of human health and the environment at these sites. In some cases, the RPM consider if risk management (e.g., institutional controls and containment) may be the most effective method of eliminating exposure pathways at complex sites. The Interstate Technology and Regulatory Council (ITRC) has recommended an adaptive site management approach for complex sites. Adaptive site management is a comprehensive, flexible, and iterative process that is well suited for sites where there is significant uncertainty in remedy performance. This process includes the establishment of interim objectives and long-term site objectives that consider both technical and non-technical challenges. Periodic adjustment of the remedial approach may involve transitioning from aggressive source and/or containment technologies to passive treatment or monitored natural attenuation over time (often referred to as a “treatment train”). RPMs plan for evaluations to actively track remedy progress and to improve the timeliness of remedy optimization or technology transitions. More information can be found in ITRC Remediation Management of Complex Sites.

Various risk management approaches can be incorporated as components of the adaptive site management framework. Approaches can include applicable or relevant and appropriate requirement (ARAR) waivers, technical impracticability (TI) waivers, state designations (e.g., plume management zones), alternate concentration limits (ACLs), and groundwater reclassification. For example, alternative endpoints are formal designations for alternate remedial goals that are permitted by regulations. These alternate remedial goals allow cleanup decisions to be based on site-specific exposure and risk, rather than defaulting to a commonly applied value such as a maximum contaminant level (MCL) where groundwater does not serve as a drinking water source. Adaptive approaches can also be used to meet traditional endpoints over the long term such as monitored natural attenuation (MNA) over extended timeframes and low-threat or risk-based closure. More information on alternative endpoints, TI waivers, ACLs, and other risk management approaches can be found in Chapter 8 of the Department of the Navy (DON) Environmental Restoration Program (ERP) Manual.



Title and Description

ERP Manual

DON Environmental Restoration Program Manual: Chapter 8 Remedial Investigation/Feasibility Study (February 2018)
Describes alternative endpoints, ARAR waivers, TI waivers, and other risk management approaches that can be applied at ER sites.

RAA Guidance

Naval Facilities Engineering Command Guidance for Remedial Alternatives Analysis (October 2020)

This guidance document describes the requirements for RAAs, the procedures for RAA preparation, and the review process for RAAs. This document updates the RAA guidance issued in April 2012. A detailed template for preparing the RAA is attached

Document Review

NAVFAC ER,N Program Directive for Quality Document Review (QDR) of DON Installation Restoration Program (IRP) Sites (June 2018)

Summarizes the process for obtaining the required internal reviews of key documents.

ARARs, Waiver

NAVFAC Toolkit for Identifying ARARs (August 2014)

Contains eight graphical exhibits to aid in outlining the key concepts in identifying and documenting ARARs.

Remedial Alternative 
Analysis (RAA)

DON Policy for Optimizing Remedial and Removal Actions at all DON Environmental Restoration Program Sites (April 2012)

Clarifies when optimization reviews are necessary and provides effective remedial strategies to meet remedial action objectives. As part of the remedial alternatives analysis (RAA), DON policy requires approval for the installation of a pump-and-treat system at an ERP site.


Title and Description

In-Situ Remediation

Electrokinetic-Enhanced In Situ Remediation Fact Sheet (2023)
Electrokinetic (EK)-enhanced in situ remediation offers a promising approach to treating source zones at complex sites such as those with low-permeability. This fact sheet discusses how delivery methods work and explores two case studies where EK-enhanced in situ remediation was applied. Lessons learned and considerations for applying and implementing EK technologies are also summarized.  

Well Rehabilitation

NAVFAC Webinar: Rehabilitation and Maintenance of Pump and Treatment Systems (January 2018)

This webinar provides an overview of key design aspects and maintenance practices needed to achieve optimal performance and to minimize life cycle costs for environmental remediation wells.

Well Rehabilitation

NAVFAC Production Well Construction and Maintenance Fact Sheet (April 2017)

Describes how to design and maintain functioning production wells (including groundwater extraction and reagent injection wells).


NAVFAC Webinar: Portfolio Optimization (P-Opt) Review of the Navy’s IRP Sites – Phase 1 Overview and Findings (August 2017)

This webinar combines Navy field examples and lessons learned from the P-Opt Phase I review to highlight some of the remaining challenges in the Navy's IRP.

Dilute Plumes

NAVFAC Webinar: Dealing with Dilute Plumes (April 2017)

This webinar discusses the roles of source depletion, matrix diffusion, and various natural attenuation mechanisms in determining a suitable path forward for dilute plumes.

Fractured Rock

NAVFAC Site Characterization and Remediation in Fractured Rock Fact Sheet (August 2017)

Summarizes the types of fractured rock environments, site characterization, remediation approaches, along with special considerations and lessons learned from fractured rock sites.

Alternative Endpoints

NAVFAC Webinar: Managing the Navy’s Complex Groundwater Sites: Alternative Endpoints and Approaches (April 2015)

This webinar provides an overview of alternative endpoints and approaches for groundwater remediation at complex sites.

Site Closeout

DON Remedial Action Completion Report (RACR) in the Navy's Site Closeout Process Fact Sheet (November 2014)

Clarifies how to document remedial action completion activities and site closure including groundwater sites with long-term management and land use controls (LUCs).

Chlorinated Solvents

Environmental Security Technology Certification Program (ESTCP) Frequently Asked Questions Regarding Management of Chlorinated Solvents in Soils and Groundwater (July 2008)

Contains commonly asked questions when selecting remedies for chlorinated solvent sites and offers a concise overview of technical challenges faced with subsurface chlorinated solvent releases.

Risk Management, ACL, TI Waiver

NAVFAC Groundwater Risk Management Handbook (January 2008)

Provides an overview of challenging site conditions for groundwater plumes and summarizes risk management strategies such as establishing points of compliance (POCs), ACLs, performing mixing zone analyses, and TI waivers.

DNAPL, Source Zone

NAVFAC DNAPL Management Overview Handbook (April 2007)        Provides an introduction on how to manage DNAPL contamination at a site. Because DNAPL sites can be very challenging, this document focuses heavily on the limitations of characterizing and removing DNAPL and how to make realistic management decisions in the midst of these uncertainties.


Title and Description

Monitored Natural Attenuation

Development of a Quantitative Framework for Evaluating Natural Attenuation of 1,1,1-TCA, 1,1-DCA, 1,1-DCE, and 1,4-Dioxane in Groundwater (ER-201730)
This project developed a new fate and transport model to easily evaluate historical monitoring data to predict biodegradation rate constants as well as new decision matrices (flowcharts) that serve as a guided tour on how to interpret potential lines of evidence for MNA. The project objectives were to; Develop a modified model and framework for evaluating natural attenuation of these compounds. Develop and validate a protocol to directly measure rate constants for natural biodegradation of 1,4-dioxane using 14C- labeled 1,4-dioxane and groundwater from 10 different field sites. Use the field and laboratory data to establish if there is consistency between various lines of evidence for 1,4-dioxane attenuation.

Chlorinated Solvents


Protocol for Selecting Remedies for Chlorinated Solvent Releases (ER-200530)

This guide is intended to assist decision makers with selecting remedies for releases of chlorinated solvents to the subsurface environment. Content includes a review of the nature of the problem, consideration of the critical components of setting objectives, a current overview of available options, and suggestions for developing comprehensive remedial packages.

Fate and Transport


United States Geological Survey (USGS) Groundwater Software

Models in the public domain that can be used to understand groundwater flow (e.g., MODFlow) and the fate and transport of contaminants in the subsurface (e.g., MT3D).

Matrix Diffusion 

ESTCP Matrix Diffusion Toolkit

Calculates and evaluates matrix diffusion effects to determine if these processes are significant enough to cause rebound of downgradient plume concentrations above remedial goals after remediation.


Chlorinated Solvent

Matrix Diffusion 


A software application used for simulating the transient effects of groundwater source and chlorinated solvent plume remediation that takes into account matrix diffusion.

Environmental Restoration



Enviro Wiki Webpage

This webpage makes scientific and engineering research results more accessible to the target audiences, facilitating the permitting, design and implementation of environmental projects. Articles are written and edited by invited experts to summarize current knowledge for environmental professionals on an array of topics, with cross-linked references to reports and technical literature.

CSM Checklist

Conceptual Site Model (CSM) Considerations - Terrestrial/Groundwater 

A CSM checklist for groundwater and terrestrial considerations.

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