Prioritizing Floodplains to Restore the Health of the Mississippi River Basin.

By ISS Expedition (NASA Earth Observatory) via Wikimedia Commons

In Brief

Nearly all the floodplains in the Mississippi River Basin (MRB) have been converted from natural ecosystems to agriculture or development and are hydrologically disconnected and degraded. Floodplain restoration will be critical to restoring the health of the MRB and reducing the hypoxic zone in the Gulf of Mexico. Although more funding and capacity are needed to greatly increase the scale and pace of floodplain restoration, decision-making can be informed by the Floodplain Explorer, a new online tool that helps prioritize important areas for floodplain conservation and restoration projects.

Key Concepts

  • The Mississippi River Basin and its tributaries have been profoundly transformed through human modification.

  • Excessive nutrient loading and a lack of connected floodplain habitats in the Basin contribute to hypoxic conditions in the Gulf of Mexico.

  • Floodplain restoration could reduce nutrient loss, support fish and wildlife habitat, store carbon, and provide a host of benefits to communities throughout the Mississippi River Basin.

  • Targeted policy and programmatic actions could enhance funding, capacity and incentives for floodplain conservation and restoration projects.

  • An interactive mapping tool has been developed to help identify strategic floodplain opportunities to improve environmental conditions in the Mississippi River Basin.

The Problem
The Gulf of Mexico set a record in 2017: it contained an area of water the size of New Jersey (22,729 km2) that could not support life. Aptly named the “Dead Zone”, the water near the bottom of the ocean in this area is very low or devoid of oxygen (i.e., hypoxic). The Dead Zone not only impacts the ecological systems in the Gulf, but can also disrupt the distribution and growth of important commercial fisheries.1 This disruption affects market price and profitability in regional fisheries and, therefore, the local economies that rely on healthy oceans and coasts.2 Unfortunately, this phenomenon is nothing new. First discovered by shrimp trawlers in the 1950s, the Dead Zone has been a recurring phenomenon each summer off the coast of Louisiana, with its size now documented annually by National Oceanic and Atmospheric Administration scientists. The primary cause of the Dead Zone is excess nitrogen and phosphorus from farms and cities that are discharged to the Gulf via the Mississippi River.3 The nutrients cause enormous blooms of algae that eventually die, fall to the ocean floor and are decomposed by aerobic microbes, a process that consumes much of the oxygen, creating hypoxic conditions.3,4

The Dead Zone itself is merely a symptom of the broader problem; the Mississippi River Basin (MRB) has been so profoundly transformed that it no longer functions as a healthy river system. The Mississippi River itself and its major tributaries have experienced tremendous change over the past century, with tens of millions of hectares of floodplain habitat across the basin developed or converted to agriculture.5-7 While the river was used to facilitate the lead, freight, and transportation industries of the 1800s, major river engineering modifications began in earnest after the catastrophic flood of 1927.8 The Mississippi River and Tributaries Project (MRT) was implemented in response to the 1927 flood, and began the ongoing process of converting the river into a highly engineered system designed to protect communities and agricultural lands against river flooding and to maintain a stable, efficient navigation channel.9 Since the MRT, thousands of additional kilometers of levees, backwater areas, floodways, training structures and channels have been constructed to help mitigate flooding in some places, but have unintentionally exacerbated flooding elsewhere in the basin.10-15 Modification of the hydrologic regime has also encouraged extensive floodplain development throughout the entire MRB.16 Now only 10% of the original floodplain area experiences active river flow because the connection between the floodplain and the river channel has been severed.11,17 Forested wetlands along the Mississippi and coastal habitats in Louisiana have been dramatically reduced both in size and extent and the remaining MRB floodplain forests are more isolated, less diverse, and less functional than they were prior to European expansion.18,19 The degradation, conversion and hydrologic disconnection of natural floodplains in the MRB has significantly altered many natural processes, including sedimentation and nutrient cycling, carbon storage and greenhouse gas fluxes, and the formation of habitats that support a variety of terrestrial and aquatic species.18-20

These large-scale changes to the structure and function of the MRB lead to problems throughout the MRB. Intensive agricultural production causes local water quality impairment that impacts drinking water supplies, habitat for wildlife, and people’s ability to recreate in nearby lakes, rivers, and streams.21-23 Additionally, disconnection between the river and its natural floodplain enhances river stage volatility, meaning that water levels can fluctuate rapidly, from very low stages to very high stages and vice-versa. This rapid fluctuation makes areas of the river system increasingly vulnerable to extreme hydrologic events.11,24 Several impactful floods in the basin have occurred in the past 25 years, including in 1993 (48 deaths, $36 billion in estimated costs), 2008 (24 deaths, $12 billion), 2011 (12 deaths, $5.5 billion), and 2017 (20 deaths, $2 billion).25 Because of the extensive modifications and degradation of the MRB, this basin received an overall grade of D+ on a “report card” developed by a broad coalition of experts and stakeholders from more than 400 organizations, businesses, state and federal agencies and academia.26 Thus, there is a great need to develop and implement solutions that can reduce nutrient loads to the Gulf of Mexico and ultimately reduce the hypoxic zone, restore critical habitats for fish and wildlife, and address localized problems of water quality and quantity.

The Solution
Large-scale floodplain restoration throughout the entire river system will be a key solution for addressing the multiple challenges facing the MRB. Floodplains are unique places where fluctuating river flows and periodic inundation form dynamic connections between the aquatic world of the river and the terrestrial world of the surrounding landscape.6 This interface between land and water creates a wide array of habitats that support high plant and animal biodiversity.27 Floodplains also can improve river water quality by removing nitrogen from floodwaters through denitrification, and by retaining sediment, phosphorus, and other harmful contaminants like heavy metals and industrial chemicals from surface waters.28-30 Additionally, floodplain ecosystems store substantial reserves of carbon, can store and convey water to mitigate flood damages, and provide a range of other valuable benefits, such as supporting fish nurseries and wildlife habitat.22,31


Fig. 1 Map showing the locations of the three floodplain projects.


We know floodplain restoration can provide these benefits because we have documented the impacts on sites where The Nature Conservancy (TNC) and its partners have been working to improve floodplain conditions over the last two decades (Fig. 1). For example, TNC led the restoration of a 2,723-hectare farm along the Illinois River now known as Emiquon Preserve (Fig. 2). Once a broad floodplain consisting of expansive fluvial lakes, this area was disconnected from the Illinois River, turned into a drainage and levee district, and converted to agricultural fields that were drained by a system of subsurface drainage tiles (underground pipes) and pumps.32 Floodplain restoration on Emiquon began in 2007 and consisted of returning the agricultural fields to lakes and wetlands, planting native vegetation, and stocking 32 native fish species to augment natural regeneration and recolonization of the floodplain. After purchasing the property, TNC stopped pumping the water out of Emiquon which restored the hydrology and allowed the lakes to refill. In 2016, TNC built a water control structure to re-connect the river to its original floodplain. Restoring public use of these important wetlands resulted in a vibrant outreach and education program. Initial monitoring of hydrology, fish, mussels, water birds, and other key targets has showed positive and encouraging results. Two years after the start of the project, nearly 1,700 ha of wetted areas (moist soil, wetlands, and lakes) had been restored, and eight years after restoration, 46-55% of monitored indicators were within target ranges.33


The Nature Conservancy
Fig. 2 The Emiquon Preserve (right) and the Illinois River (left) between the towns of Havana and Lewistown, Illinois. Photo shows the water control structure built in 2016 to restore connection of the restored wetlands to the Illinois River.


Additional research shows that Emiquon’s wetland soils are storing carbon (38.29 Mg C ha-1) and nitrogen (TN – 1.43 Mg N ha-1), though at levels significantly lower than reference wetlands.34 Public use data show 27,000 people visited Emiquon in 2015 (8-years post restoration), including boaters, hunters, fishers, and visitors attending educational programs32 and more than 40,000 people visited in 2017 (D. Blodgett, personal comment). Progress on the restoration objectives show that the Emiquon project has been successful, revealing the potential for successful floodplain restoration, even within a highly degraded and disconnected system such as the Illinois River.


The Nature Conservancy
Fig. 3 Mollicy Farms (left) prior to reconnection with the Ouachita River (center). Before it was converted for agriculture, Mollicy was a mature floodplain forest, like that shown on the right of the photo.


More than a thousand kilometers further south in the MRB, The Nature Conservancy has worked with partners to reconnect and restore 6,500 hectares (ha) of former farmland to native floodplain forest. Mollicy Farms was once part of a vast expanse of floodplain forest seasonally inundated by the floodwaters of the Ouachita River in northern Louisiana (Morehouse Parish) (Figure 3).35 In the 1960’s, the area was deforested and converted to agriculture and separated from the river via a 9 m high, 27 km long levee. Additionally, bayous (slow moving lowland streams) that transmitted river water through the floodplain were severed, blocked, and replaced with a network of drainage canals. From 1990-1998, TNC helped the U.S. Fish and Wildlife Service acquire 6,500 ha of Mollicy Farms and add it to the Upper Ouachita National Wildlife Refuge. Together the US Fish and Wildlife Service and TNC planted over three-million trees to restore the floodplain forest. In 2009-2010, TNC and partners removed portions of the levee to reconnect the former floodplain to the Ouachita River, and completed hydrologic restoration in 2013 by reconstructing the historic bayous, plugging the drainage canals, and removing other flow impediments. The levee removal and other actions restored hydrology across the project site and in upstream sub-watersheds, increasing the restoration footprint to over 30,000 ha. This large reconnected floodplain reduced peak stage in the Ouachita River during a record flood by 0.3 m in 2009.36 Mollicy Farms has removed ~ 48.1 Mg of nitrogen (N) from the Ouachita River annually in the last six years. The current NO3-N reduction rate (11.8 ± 3.37 mg N m−2 d−1) is now only 28% lower, than undisturbed, mature floodplain immediately across the river.37 These N removal results at Mollicy Farms demonstrate the effectiveness of floodplain restoration as a nutrient removal strategy.

The Atchafalaya River Basin (ARB) in Louisiana, located about 402 km south of Mollicy Farms, is the largest intact floodplain remaining in the Mississippi River Basin.38 At about 405,000 ha, it provides critical habitat for fish and wildlife as well as a myriad of nature-based services for people (e.g., flood protection, navigation, commercial fisheries, recreation, CO2 sequestration). As the principal distributary of the lower Mississippi River, the Atchafalaya River delivers about 375,000 MT of N to the Gulf of Mexico annually, making the vast floodplain wetlands of the ARB a key area for floodplain restoration and nutrient removal.38 However, intensive water management and hydrologic alteration of the ARB, that began in the 1930s and continue today, have interrupted natural flow, flooding, and drainage patterns. Such alteration has changed sedimentation patterns and nutrient cycling, causing the formation of extensive hypoxic zones within the floodplain that impact forest health, regeneration, and biotic resources.38,39 For example, growth of red-swamp crayfish (Procambarus clarkia) that support the largest commercial fishery in the ARB is 50% slower in hypoxic conditions, showing the importance of healthy floodplain habitats to the local economy.40,41 Nutrient sequestration rates for forested wetlands in the ARB also have been decreased by the alteration of water flow patterns.38,42 In 2015, TNC established the Atchafalaya Basin Preserve, initiated efforts to restore hydrology across the ARB, and established a long-term comprehensive monitoring and applied research program. Its first restoration project is currently underway and aims to restore natural water flow patterns across 2,225 ha of floodplain forest on the Preserve and surrounding state-owned lands. Pre-project monitoring and research results show that restoration is expected to increase the annual duration of floodplain connectivity five-fold (~ 20 – 120 days per year), improve forest health [e.g., improved forested floristic quality index, increased propagation and growth of baldcypress (Taxodium distichum) and water tupelo (Nyssa aquatica)], and sequester nutrients at a rate of ~ 59 mg N m-2 d-1, totaling 107 MT of N over a three-month flooding period across the project area.43

These projects illustrate the effectiveness of current floodplain restoration activities and the potential for scaled-up restoration to contribute to efforts to reduce the size of the Dead Zone, improve local water quality and restore the habitats and ecosystem functions of the MRB. They show that by reconnecting floodplains to their channel and restoring their natural hydrology, floodplain restoration projects can return native perennial vegetation, reestablish wildlife and fish populations, improve local water quality and quantity, and provide beauty and enjoyment for the public. A primary challenge to using floodplain restoration to improve water quality and quantity, habitat, and the health of the MRB and Gulf of Mexico is identifying where to target investment of the currently limited funding.

The Floodplain Explorer
To address this challenge, the Nature Conservancy is developing the “Floodplain Explorer” (, an interactive web-based and data-driven decision support tool designed to help state, regional, and local stakeholders identify and prioritize areas where floodplain conservation and restoration are most needed and likely to be most effective. The Floodplain Explorer integrates multiple spatial data sets that characterize important functions and valuable benefits provided by floodplains. First and foremost, the tool provides a comprehensive mapping of floodplain extents at both the 1% chance and 20% chance flood events (the so-called “100-year” and 5-year floods, respectively), drawing upon detailed data derived from a regional, physically-based hydrodynamic flood model.44 The Floodplain Explorer then uses an array of other data and model outputs to identify priority floodplains for either conservation or restoration, based on the potential of these areas to provide multiple benefits. For example, we used SPARROW model outputs to characterize floodplains located in areas contributing high quantities of nutrients to the Gulf of Mexico and local waterways.45 We supplemented this nutrient loading information with an assessment of where we expect floodplains to most effectively remove these nutrients, using estimates of inundation duration, accumulated growing degree days, and soil organic matter.46-48 We included stream habitat disturbance estimates, U.S. Fish and Wildlife Service data regarding critical habitat for threatened and endangered species (, and EnviroAtlas at-risk wetland species data (, to incorporate information related to wildlife habitat and species of conservation concern.49 We also integrated spatial data provided by a recent analysis that mapped current and projected future development in floodplains and quantified estimated flood damages and population exposure.50 To highlight floodplain areas at risk of becoming urban or agricultural land in the future, we used land use change projection models from the US Environmental Protection Agency ICLUS project and the Land Transformation Model.51, 52 Finally, we used a national dataset of average land value to map the estimated cost of land acquisition, which is a key component of the cost of floodplain restoration projects.53,54 We have identified these and other relevant data sets by working with stakeholders throughout the MRB to solicit information on best-available floodplain data and the information needs of relevant decisions. Using this information we are developing the Floodplain Explorer to provide a useful, dynamic platform that enables users to access and integrate these multiple data sets to prioritize opportunities for floodplain conservation and restoration. The tool will allow the user to interactively choose the subsets of the above data layers of interest to them – nutrient removal, habitat, estimated flood damages, etc. – and view the resulting effects on the portfolio of priority sites identified throughout the basin. In this way, we expect the tool to help support different decisions by various stakeholders by allowing users to identify priorities and assess tradeoffs related to different floodplain restoration goals. Overall, the Floodplain Explorer is designed to provide relevant, actionable information that can improve decision-making and resource allocation to help prioritize and coordinate effective floodplain restoration in the MRB.

Funding strategies
The Floodplain Explorer takes a critical step toward addressing a real barrier to large-scale floodplain restoration by providing valuable information about where to prioritize restoration actions. However, there are insufficient funds to match the scale of restoration with the scale of the problem. Together the projects described above only add up to approximately 35,000 ha, but as many as 2.2 million ha of restored wetlands may be needed to help meet nutrient reduction goals and reduce the Gulf of Mexico hypoxic zone.55 The lack of resources is daunting, yet there are three key areas where targeted policy and programmatic actions could enhance funding for floodplain projects.

First is the Agricultural Act of 2014 (P.L. 113-79, the “Farm Bill”), the primary policy tool of the federal government that is used to influence trade, commodities, conservation, research, food, and other issues related to agriculture. The Farm Bill contains several conservation programs that could be fully funded and expanded when the legislation is renewed. For example, if the Wetland Reserve Easement program under the Agricultural Conservation Easement Program (ACEP-WRE) were expanded and increased to at least $500 million over the next 10-years, critical funding and technical assistance could be applied to retire agricultural lands that could restore and reconnect floodplains. Additionally, restoration of the Conservation Reserve Program (CRP) to its former higher acreage cap of 14.2 Mha, could also support voluntary agricultural land retirement. The administration of both CRP and ACEP-WRE programs could be enhanced so that payments could be prioritized for retirement of lands, like floodplains, likely to provide the greatest benefits. Together these programs offer a far-reaching and effective mechanism to increase funding for floodplain projects.

Second, Congress could support several important opportunities to catalyze greater floodplain restoration in the MRB by authorizing and funding U.S. Army Corps of Engineers restoration programs. For example, the Navigation and Ecosystem Sustainability Program (NESP) was authorized in the Water Resources Development Act (WRDA) of 2007, but no funding has ever been appropriated for construction. If Congress fully appropriated NESP funding, the program could help reconnect nearly 15,000 ha of floodplain in the Upper Mississippi River basin, restoring vital areas of floodplain forest and wetlands that will contribute to significant in-stream nutrient reductions. The current restoration program – the Upper Mississippi River Restoration Program (UMRR) – is enabling restoration of about 1,200 ha of floodplain annually and supports important scientific and program management capacity that would be essential to ramp up floodplain restoration efforts when NESP is fully funded. Full appropriations for UMRR is essential for continued floodplain restoration throughout the Upper Mississippi River until such time that NESP receives funding that exceeds the current restoration and monitoring dollars of UMRR. Congressional authorization of the Lower Mississippi River feasibility study in the 2018 WRDA legislation and eventual funding would establish parameters for a main stem water quality monitoring program and prioritize restoration of side channels, oxbows, and bayous on nearly 1,600 km of the Lower Mississippi River.

Third, several important Federal Emergency Management Agency (FEMA) programs could be expanded to help spur investment in proactive and nature-based approaches to flood risk reduction. For example, the Pre-Disaster Grant Mitigation Program is the only FEMA program that provides funding for projects before a flood disaster has occurred. This program enables communities to seek funding for hazard mitigation planning and a variety of risk reduction activities, including acquisitions of repetitive loss properties and restoration of open space in floodplains. The Flood Mitigation Assistance Grant program, designed to fund projects that reduce claims to the National Flood Insurance Program, provides another opportunity to support floodplain projects. If funding for both programs were increased by Congress, they would enhance communities’ ability to proactively reduce flood risk while also supporting greater use of floodplains as natural infrastructure.

By addressing these three areas of improvement through increased funding and implementation, floodplain restoration could be significantly advanced in the MRB. Improved zoning, better land use planning, and other policies and programs at the state and local level could also catalyze more floodplain projects. Yet notwithstanding the need for increased funding and programmatic capacity, it is essential to prioritize investment of limited resources to ensure that floodplain projects deliver the best bang for the buck. The Floodplain Explorer provides a promising tool that should help decision-makers around the MRB identify the greatest opportunities for floodplain restoration.


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