research projects

Coupling lake, watershed, and estuarine models to better understand the role of engineered freshwater discharges in driving the severity, location, and timing of harmful algal blooms

Sponsor: U.S. Army Corps of Engineers Engineering Research and Development Center, Principal Investigator: David Kaplan (, Start Date: October 2021, Project Size: $2.3 million.

Severe freshwater and marine harmful algal blooms (HABs) in Florida’s lakes, rivers and estuaries have resulted in tremendous environmental and economic damages in recent years. In southwest Florida, blooms are becoming more frequent, more damaging, and longer lasting, threatening the health and well-being of coastal communities. The goal of this project is to develop data- and model-supported guidance for water management to prevent or reduce the impact of harmful algal blooms across the region, which responds to an increasing call for more scientifically supported water- and nutrient-management strategies, particularly for Lake Okeechobee.  This project is led by CCS Associate Director Dr David Kaplan and involves Dr. Elise Morrison (UF, ESSIE), Dr. Edward Phlips (UF| IFAS), Dr Natalie Nelson (North Carolina State University), Maurcio Arias (University of South Florida) and Dr. Eric Milbrandt (Sanibel-Captiva Conservation Foundation).  

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Social-Ecological Effects of Hydroelectric Dams in the Brazilian Amazon 2014-2019

Funded by the UF Office of Research, CAPES – Brasil, and the UF Water Institute. The Amazon basin hosts an extremely valuable conglomeration of ecological and social systems, harboring complex feedback systems and providing innumerable ecosystem services. The Brazilian government plans the rapid development of a vast network of hydroelectric dams and supporting infrastructure in the Amazon over the following decades. This will not only directly impact river hydrology and biology, but will also generate land-use changes, such as deforestation, that will impact the hydrologic cycle and biodiversity on a regional scale, driving the likely loss of myriad ecosystem services. In October 2014, a team of UF faculty from the Amazon Dams Network (ADN) was awarded the 2015 Water Institute Graduate Fellows (WIGF) Program to study the complex and interactive set of impacts brought about by the construction and operation of dams and other hydraulic infrastructure in the Amazon. The ADN team’s proposal, “Hydrologic transformation in the Amazon basin: reconciling economy, society, and the environment in the world’s largest watershed” is led by Dr. Kaplan with co-PIs Stephanie Bohlman, and Denis Valle (School of Forest Resources and Conservation), Kai Lorenzen (School of Natural Resources and Environment), and Cynthia Simmons and Bob Walker (Geography). The award supports six new Ph.D. students beginning in 2015, with recruitment beginning immediately.

Managing Forests for Increased Water Yield 2012-2018

Funded by all five Florida Water Management Districts, FL Department of Agricultural and Consumer Services. While the perceived benefits of forest management are often limited to habitat improvement, specific management actions that reduce forest biomass (from thinning and prescribed fire) may also have implications for regional water yield. Because evapotranspiration (ET) dominates ecosystem water losses in the southeastern US, even modest reductions in the proportion of rainfall lost to ET (e.g., from 90% to 80%) can result in large fractional increases (e.g., doubling) in water yield. In previous work, we developed a statistical model of water yield as a function of management strategy, stand structure, and ecosystem water use. Results suggested a potential increase in water yield of up to 64% for pine stands managed at lower basal relative to systems managed for high-density timber production, but identified critical sources of uncertainty, including the effects of climatic variation, between-site variability, water use in young pine stands, and prescribed fire. In upcoming work, we aim to reduce uncertainty around projected water yield subsidies from modified management. To quantify the effects of land management on forest biomass, ET, and water yield, we will apply a comparative evaluation across a gradient of environmental conditions (soil type, aquifer confinement, and climate). Within each site, treatments (i.e., plots) target variation in management activities (e.g., thinning, clearcutting, and fire) and forest biomass. Groundwater and soil moisture data are used to construct daily vadose zone and aquifer water budgets to determine ecosystem ET and water yield. Preliminary total ET data from a slash pine stand in north central Florida show good agreement with independent ET estimates derived from eddy correlation measurements, suggesting that this relatively low-budget approach can provide ET measurements at scales and costs requisite for understanding the role of land on local and regional water yield.

Nitrate Cycling and Hydraulics in Florida Springs 2013 – 2017

Funded by St. Johns River Water Management District, University of Florida University Scholars Program. One of the most pressing issues facing Florida’s waterways is anthropogenic nitrate pollution due to more than fifty years of rapid population growth and increased agricultural activity. In light of recently declared numeric nutrient criteria, an understanding of nutrient cycling processes is crucial for proper water management practices. In-stream nitrate removal due to denitrification is thought to be positively correlated with high velocity gradients and increased hyporheic exchange. However, previous studies in tidally influenced springsheds have noted greater nitrate retention at lower velocities possibly due to increased residence times. This study aims to identify the connection between water velocity, hyporheic exchange, and nitrate removal rate using the biologically reactive tracer resazurin to directly measure the amount of spring discharge subject to hyporheic exchange under varying flow conditions. Tracer studies will be performed during various stages of the tidal cycle and breakthrough curves of resazurin and its byproduct resorufin will be analyzed and compared to in situ nitrate measurements to determine the contributions of residence time and hyporheic exchange to nitrate cycling. Identifying the driving hydraulic force in denitrification could aid in future restoration and water treatment decisions as well as predictions of how aquatic ecosystems will respond to changing hydrologic conditions including flooding, drought, and groundwater recharge and depletion.

Estuarine Freshwater Entrainment By Oyster Reefs: Quantifying A Keystone Ecosystem Service 2013 – 2015

Funded by Florida SeaGrant. Oyster reefs have been shown to provide myriad critical ecosystem services, however their role in directing flow and currents during non-storm conditions has been largely neglected. In many regions, oyster reefs form as linear structures perpendicular to the coast and across the path of streams and rivers, potentially entraining large volumes of freshwater flow and altering nearshore mixing. We hypothesize that these reefs have the potential to influence salinity over large areas, providing a “keystone” ecosystem service by supporting multiple estuarine functions. Here we present results from a field and modeling study to quantify the effects of reef extent and elevation on estuarine salinities under varying river discharge. We found salinity differences ranging from 2 to 16 g/kg between inshore and offshore sides of degraded oyster reefs in the Suwannee Sound (FL, USA), supporting the role of reefs as local-scale freshwater dams. Moreover, differences between inshore and offshore salinities were correlated with flow, with the most marked differences during periods of low flow. Hydrodynamic modeling using the 3-D Regional Ocean Modeling System (ROMS) suggests that the currently degraded reef system entrained greater volumes of freshwater in the past, buffering the landward advance of high salinities, particularly during low flow events related to droughts. Using ROMS, we also modeled a variety of hypothetical oyster bar morphology scenarios (historical, current, and “restored”) to understand how changes in reef structure (elevation, extent, and completeness) impact estuarine mixing and near-shore salinities. Taken together, these results serve to: 1) elucidate a poorly documented ecosystem service of oyster reefs; 2) provide an estimate of the magnitude and sptial extent of the freshwater entrainment effect; and 3) offer quantitative information to managers and restoration specialists interested in restoring oyster habitat.

Hydrological, Ecological and Human Drivers of Coastal Change 2012 – 2016

Funded by US Fish and Wildlife Service, Florida Department of Economic Opportunity. Sea level rise (SLR) is a growing concern ecologically and economically for coastal communities in Florida and around the world. Coastal regions are particularly susceptible to local changes in sea level resulting from increased temperatures, changing winds and currents, and subsidence. This study examines the interacting effects of SLR, climate change, groundwater supply, and land use on saline and freshwater vegetation communities along the Big Bend region of Florida. Data from hydrological monitoring and vegetation transects will be collected at three primary locations along Florida’s Gulf Coast: Lower Suwannee National Wildlife Refuge, Waccasassa Bay, and Withlacoochee Bay. Previous vegetation data collected in Waccasassa Bay will be pooled with this current research to conduct a long-term analysis on the impacts of SLR and salt water intrusion on species composition and population dynamics in coastal forests. Field data will be supplemented with publicly available data on vegetation communities, species composition, land use, and topography in Withlacoochee Bay to create a baseline against which future SLR impacts can be projected. This study also includes the development of long-term adaptation strategies for incorporation into municipal policy and planning documents to help coastal communities preserve natural resources vulnerable to SLR.

Florida’s Participation in the National Wetland Condition Assessment 2011-2014

Funded by US Environmental Protection Agency. The US Environmental Protection Agency (EPA) has embarked on a nationwide National Aquatic Resource Survey (NARS) to access the condition of the Nation’s lakes (field work in fiscal year (FY07), rivers (FY08), streams (FY09), coastal waters (FY10), and wetlands (FY11). As part of the larger NARS project, the University of Florida-H.T. Odum Center for Wetlands (UF-CFW) project specifically focuses on participation in the statewide assessment of wetland condition as part of the US EPA National Wetland Condition Assessment (NWCA) 2011. Information collected from this assessment will be used by the US EPA in support of the first ever nation-wide evaluation of wetland condition based on chemical, physical, and biological parameters. The NWCA uses a probability-based sample design, resulting in a statistically valid estimate of condition for a population of wetlands. During the execution of the NWCA, Level II Rapid Assessment and Level III Intensive Site Assessment will be conducted through the Level II US Rapid Assessment Method (US-RAM) and Level III field and laboratory studies on algae, vegetation, water and soil chemistry, hydrology, and buffers.

Water Monitoring Program Enhancements and National Wetland Condition Assessment 2011-2014

Funded by US Environmental Protection Agency. The University of Florida-H.T. Odum Center for Wetlands (UF-CFW) in cooperation with the monitoring and assessment needs of the Florida Department of Environmental Protection (DEP) with funding through the US Environmental Protection Agency (US EPA) have begun work to supplement the National Wetland Condition Assessment (NWCA) 2011. Funds from this grant will be used for monitoring program improvements within Florida. The funds will enhance FDEP’s ability to assess waters, report on overall condition, and obtain the needed water quality information to develop and assess protective numeric water quality criteria. Four specific project tasks include further development of statistically-valid assessments of waters, procurement of monitoring equipment (i.e. dissolved oxygen probes), enhancements to biological monitoring (e.g. field testing of Florida Wetland Condition Index (FWCI) against NWCA, determination of temporal variability in vegetation), and monitoring to support development of water quality criteria.

Level 1 Landscape Scale Analysis of Wetland Condition 2011-2014

Funded by US Environmental Protection Agency Region IV. This project builds on the US Environmental Protection Agency (EPA’s) National Wetland Condition Assessment (NWCA) 2011 by performing geographic information systems (GIS) based site evaluation and a Level I Landscape Assessment of 67 wetland assessment points located within the state of Florida. Through the use of the Level I Landscape Assessment using the Landscape Development Intensity (LDI) index this project seeks to link the Level II Rapid Assessment and Level III Intensive Site Assessment with the landscape scale and demonstrates a remote office based tool to evaluate wetland condition to support monitoring capacity of the state’s wetland resources.

Past research projects (2000-2010)

Isolated Wetlands and “Significant” Nexus

Funded by US Environmental Protection Agency. Recent rulings by the U.S. Supreme Court have limited federal protection over isolated wetlands, requiring documentation of a “significant nexus” to a navigable water body to ensure federal jurisdiction. Despite geographic isolation, isolated wetlands influence surficial aquifer dynamics that regulate baseflow to surface water systems. To explore the importance of this function at the landscape scale, we integrated models of soil moisture, upland water table, and wetland stage to simulate the hydrology of a low-relief, depressional landscape. We quantified the hydrologic buffering effect of wetlands by calculating the change in standard deviation of water table elevation between landscapes with and without wetlands for different soil types (see fig. for (a) sand, (b) sandy loam, and (c) loam). Increasing wetland area and/or density reduced water table variability relative to landscapes without wetlands, supporting the idea that wetlands stabilize regional hydrologic variation, but also increased mean water table depth because of sustained high ET rates in wetlands during dry periods. Considering the influence of regional water table on downstream systems, these results suggest that isolated wetlands help regulate regional surface waters through an indirect, but significant nexus. Read the paper in Water Resources Research.

Lake Jesup Total Phosphorus (TP) Removal Treatment Technologies. Floating Island Pilot Project

Funded by St John’s River Water Management District. A research project to build and test a pilot-scale floating modular treatment system consisting of interchangeable biological and physical-chemical treatment modules for TP removal from tributaries to Lake Jesup.

Summary of the Available Literature on Nutrient Concentrations and Hydrology for Florida Isolated Wetlands

Funded by Florida Department of Environmental Protection. (Report)

Wetlands on Clay Settling Areas

Funded by Florida Institute of Phosphate Research. This research project was a five-year investigation of wetlands on Clay Settling Areas (CSAs) to develop knowledge and understanding of their ecology and hydrology for establishing functional wetlands and to suggest ways to enhance their creation. The project documented the current status and historical trends of wetlands naturally establishing on CSAs, evaluated CSA hydrologic regimes, evaluated CSA ecohydrology, developed temporal and spatial hydrologic models of wetlands on CSAs, conducted short- and long-term field trials that documented survival and growth of herbaceous and forested wetland plant species, and synthesized project findings into guidelines for enhancement of existing wetlands and the creation of new ones on CSAs.

Development of Landscape Development Intensity (LDI) Coefficients for Wetlands in Little Bayou Meto Watershed in Lower Arkansas

Funded by Arkansas Soil and Water Conservation Commission. The project developed an appropriate land use classification scheme from existing Land use/land cover, collected energy and material flow data and calculated empower densities for land use classes, and developed LDI coefficients for land use classes from empower densities. (Report)

Successional Trajectories of Constructed Forested Wetlands

Funded by Florida Institute of Phosphate Research. This research addresses the development and application of the trajectory approach to assessing adequate site progress toward ecological goals for created forested wetlands on phosphate mined land.  The final report can be found on the Florida Institute of Phosphate Research’s web site:, FIPR Publication #03-142-231.

UMAM Training Manual: web based training manual for Chapter 62-345, FAC for wetlands permitting

Funded by the Florida Department of Environmental Protection. The project developed a web-based training manual designed to help users “walk-through” the process for conducting an evaluation under the newly adopted Unified Mitigation Assessment Method (UMAM). Additionally, the training manual provides some background and ancillary data on landuse, water quality, hydroperiods, and natural community guides. UMAM is now applied statewide to assess the value of wetlands and other surface waters and determine the amount of mitigation needed to offset adverse impacts. A link to the manual is available on the Uniform Mitigation Assessment Method Toolbox page from the Florida Department of Environmental Protection’s website.

2005 Pilot Study – The Florida Wetland Condition Index (FWCI): Preliminary Development of Biological Indicators for Forested Strand and Floodplain Wetlands

Funded by Florida Department of Environmental Protection. This project was a pilot study including 24 forested strand and floodplain wetlands. It developed biological indicators throughout Florida using sturctural metrics for the macrophyte community. Landscape Development Intensity (LDI) index and soil quality were also determined. The final report is available on-line through the University of Florida Digital Collections website:

The Florida Wetland Condition Index (FWCI): Developing Biological Indicators for Isolated Depressional Forested Wetlands

Funded by Florida Department of Environmental Protection. This project developed biological indicators for depressional forested wetlands throughout the entire state of Florida using sturctural metrics for the benthic diatom, macrophyte, and benthic macroinvertebrate communities.  Landscape Development Intensity (LDI) index, water quality, and soil quality were also determined.  The final report is available on-line through the University of Florida Digital Collections website:

Development of Wetland Condition Index for Isolated Depressional Herbaceous Wetlands

Funded by Florida Department of Environmental Protection. Methods to quantify the relative condition of isolated herbaceous wetlands in Florida were identified using macrophytes, macroinvertebrates, and diatoms. The metrics were combined to create the Florida Wetland Condition Index for herbaceous wetlands.

Evaluation of Successional Trajectories in Constructed Wetlands on Phosphate Mined Lands

Funded by Florida Institute of Phosphate Research.


Successional Development of Forested Wetlands on Reclaimed Phosphate Mined Lands in Florida

Funded by Florida Institute of Phosphate Research.
Studies of wetlands developing on phosphate mined lands and under controlled greenhouse conditions were conducted to evaluate the role of early successional species in ecosystem development. The project focused on primrose willow (Ludwigia peruvianna), cattail (Typha sp.), Carolina willow (Salix caroliniana), and vines. Persistence under reduced light, nutrient cycling, and nutrient sequestration were studied, as well as their role in developing and altering the physical environment (microtopography). Finally, measurable wetland attributes showing directional change with time were identified, and models of successional trajectories were established from attribute data, including tree height, dbh, canopy cover, soil organic matter content, and bulk density. The final report is available on-line from the Florida Institute of Phosphate Research:, FIPR Publication #03-131-193.

Determination of an Appropriate Onsite Sewage System Setback Distance to Seasonally Inundated Areas.

Funded by Florida Department of Health.

South Dade Stormwater Treatment Area Evaluation

Funded by South Florida Water Management District. Developed tools for the assessment of stormwater retrofitting designs in urban areas. Particular emphasis was on modeling to evaluate various conceptual plans, including geographic location of treatment sites, total area requirements, and strategies of one single vs. many small wetland systems.

Evaluation of Successional Trajectories in Constructed Wetlands on Phosphate Mined Lands

Funded by Florida Institute of Phosphate Research.