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Science Update

Connected by Water

Jane Tucker

Wil Wollheim

Christopher Whitney

We all know that water is essential for life. But how often do we consider where water comes from and where it goes? There is a whole field of science that studies that called hydrology.

Hydrologists study the constant movement of water between the atmosphere and the earth’s surface in what is called the hydrologic cycle (or water cycle). This includes how water interacts with its environment and accounts for the many forms that water can take (Fig. 2). As water moves and interacts with different environments, it also moves materials it encounters in the air or on the ground. Examples of these materials are soils important for fertile river valleys and for supplying sediment to coastal marshes and organic material whose decay releases essential nutrients into water, fueling cycles of growth and decomposition that repeat as they move downstream. Nitrate, discussed below, is one such traveler. Water may also pick up harmful things, like pollutants or plastics, or overloads of nutrients from excessive use of fertilizers.

Nitrate is an example here. The real story is about the importance of understanding hydrology - because it is through the continuous cycle of water that all places on earth are connected to and dependent on each other.

Hydrology is why a large rainstorm happening over inland urban areas or fields, or spring thaw of deep snowpack in upland forests, matters to coastal waters and marshes, sometimes many miles away. Rain and snow that fall on these landscapes are ultimately the sources of water to downstream water bodies. Some water soaks into the ground, some runs directly off the land, and some runs down gutters and streets to storm drains, but all flow down-slope toward the nearest stream or river, and ultimately to the coastal ocean. In this way, the uplands are connected to the coast - by networks of waterways, each draining its own landscape or watershed (Fig. 3), merging as they flow seaward. They are connected by water.

Figure 3. Typical forested watershed, including steams and tributaries joining to a larger river flowing through wetlands to the coast and the groundwater component.

It matters where the water travels along its path to the sea; when rain falls on the watershed, it may wash over trees, crops, lawns, rooftops or asphalt. Water will pick up substances it encounters along the way, and transport them downstream. Nitrate, a form of nitrogen, is one such substance.

Nitrogen is part of protein, which plants and animals need for growth and metabolism. That’s why we fertilize our crops and lawns with fertilizers that contain nitrogen, often in the form of nitrate. Nitrogen becomes a problem in water bodies when there is too much of it, causing algal blooms that may lead to other water quality problems. As the form of nitrogen that is most readily moved around in water, nitrate is of particular concern for coastal water bodies, so it’s important to understand how much is getting into streams and rivers, and ultimately to estuaries, and what happens to it as it is transported downstream. How much nitrate gets into water varies considerably depending on what is going on in the watershed.

One source of nitrate is in the rain itself. The Northeast has historically had high levels of nitrate in rain, snow, and other precipitation, due to air pollution from power plants in the Midwest as well as from local urban areas. Although levels have decreased in recent decades as a result of the Clean Air Act and several strengthening amendments, nitrate in precipitation remains an important input to watersheds, though levels vary with location. (For more information about the Clean Air Act, please see; for nitrogen in air pollution, please see

Nitrate may also enter waterbodies in runoff from suburban or agricultural landscapes. Overuse of fertilizers, which contain high levels of nitrate or other forms of nitrogen that are ultimately converted to nitrate, results in high levels of nitrate in water running off lawns and crops. Runoff from these landscapes often directly enters streams and rivers through drains and drainage pipes. Finally, human waste also contains nitrate, which can enter streams and rivers via septic systems and groundwater, and in discharge from wastewater treatment facilities lacking advanced nitrogen removal capabilities. For example, there are 6 municipal treatment plants along the Merrimack River, and a number of illegal discharge sites (

Nitrate is also naturally produced within soils of watersheds by certain microbes in a process called nitrification. How much nitrate accumulates in soils depends on how much these “nitrifying” microbes produce compared to how much is used by other microbes or taken up by plants, which in turn depends on soil and vegetation type, temperature and precipitation, and how much nitrate is delivered in precipitation.

Water provides the mechanism that transports nitrate from all sources to waterways, whether through man-made conduits or over land as runoff or through soils and groundwater. Slower pathways, that allow interaction with soils and vegetation along the way, can help reduce the amount of nitrate that is exported from one system to the next. For example, streams and rivers that have significant riparian buffers, where water flow slows and plants and microbes have more opportunity to take up nitrate, greatly reduce the amount of nitrogen that enters streams. In contrast, under conditions of high flow (during spring runoff or storms, for example), flow patterns become more similar to that of a pipe, with little time for biology to react (see more below). Seems to be a key point

In the Merrimack River watershed (Fig. 4), within the Gulf of Maine region, researchers from two Long Term Ecological Research (LTER) Program sites, one in Hubbard Brook Experimental Forest (HBEF) in the White Mountains of New Hampshire (Hubbard Brook LTER; HBR), and the other in the watersheds and estuaries of Plum Island Sound, Massachusetts (Plum Island Ecosystems LTER; PIE), monitor inputs of nitrate and other materials (eg. other nutrients like phosphorous, minerals like calcium, pollution indicators like mercury, and particles like sediment) to streams and rivers and study whether and how those inputs are mediated in different types of watersheds. Long term datasets like those generated by LTER programs enable researchers to evaluate trends that may be related to climate change or other controlling factors that happen on multi-year time scales.

On the regional, aggregate scale, inputs of nitrate to streams and rivers are broadly correlated with human activity, but correlations weaken as we scale down to watershed and sub-watershed (catchment) levels. The Hubbard Brook watershed for example exports low levels of nitrate overall, despite still receiving relatively high deposition from the atmosphere, but within the watershed, catchment to catchment differences remain. Many inter-related factors play into the variability, including soil characteristics, vegetation, topography, hydrology, and local climate. By incorporating site-specific factors like these, researchers can improve understanding of what controls the export of nitrate and other maybe unwanted materials from catchments to streams and inform managers.

Figure 4. Map showing the location of two LTER sites in relation to the Merrimack River watershed. Inset shows the watershed withing the GOM and New England region. Underlying map Credit NOAA Fisheries (

For example, catchments characterized by having conifers as the dominant tree species (typified by the north-facing Cone Pond catchment at Hubbard Brook) were found to be a good predictor of low nitrification rates and low inputs to streams (Ross et al., 2012). Another factor often used to predict nitrate input to streams is the level of nitrate found in soil water in areas adjacent to streams. The magnitude and timing of inputs vary within each catchment due to complex hydrology of subsurface flow and ephemeral streams, driven by seasonal climate and rainfall events interacting with soil types and bedrock.

Analyzing the extensive dataset on soil and soil water chemistry as well as hydrology that is uniquely available at HBEF, researchers found that shallow soils on steeper slopes of a catchment hillside (control catchment W3) were “hot spots” of nitrate production (red stars in Fig. 5), contributing the majority of nitrate that is exported from this catchment (Pardo et al., 2022). These soils experience fluctuations in wetting and drying, producing conditions favorable for nitrification. During periods of sufficient precipitation or snowmelt, water tables rise, creating a subsurface connection between upslope areas of production and the stream channel, and a flow path for any excess nitrate into the stream. By coupling the hot spots in the landscape with details of hydrology and climate researchers can create better predictive models to assist environmental managers.

As water continues on to the coast, where it travels and how fast it flows are important determinants on the fate of materials it carries. As described by Fazekas et al. (2021) “Hydrology changes watersheds from transformers to transporters”.

Watersheds, including their river networks, are transformers when water flow is slow and biological processing of substances like nitrate is high. Biological processes like uptake by plants, algae, and microbes on the land and in the water help reduce the amount of nitrate in the water: it may be transformed into plant and algal tissue, or transformed to other less harmful forms of nitrogen by microbes.

One microbial transformation, called denitrification, converts nitrate to nitrogen gas (an inert gas comprising 78% of the atmosphere), thereby removing it from the water. Denitrification requires oxygen-free conditions, as may be found in water-saturated soils and sediments of streams, riparian zones, wetlands, and bogs - one reason these habitats are so important to the health of rivers and streams.

In New England, the creation of wetland habitats has recently been aided by the successful repopulation of beavers. Beaver dams help slow water flow and create shallow ponds and wetlands (Fig. 6), where nitrogen transformations are enhanced. Using GIS mapping techniques, Chris Whitney (UNH PhD candidate, dissertation in prep) has shown that in the Parker River (MA) watershed, just south of the Merrimack, wetland formation increased coincidentally with increased beaver activity from1995 to 2013. This is encouraging news for the nitrogen story because wetlands have the potential to remove up to 45% of nitrate inputs (Lazar et al, 2015), preventing further transport downstream.

Figure 6 Beaver dam and pond on Cart Creek, a headwater stream of the Parker River. Photo by C. Whitney.

River networks also prevent export of nitrate downstream when biological capacity and rates of uptake within a network can keep up with the amount or rate of inputs. In a recent study using long term data from PIE and other LTER sites, and including the Merrimack, Wollheim et al. (2022) demonstrated that as water flow (input) rate increases the size of the river network becomes important. As the drainage area for a river network increases, larger rivers show disproportionally more capacity to process and hold on to nitrogen; that is, if a network triples in size, its capacity increases more than 3 times (Fig. 7).

Figure 7. As the size of a river network increases, its capacity to retain nitrogen and perform other ecosystem functions increases disproportionately. (Graphical interpretation of Fig. 1 in Wollheim et al. 2022)

Importantly, these findings suggest that the focus of input reductions should be on smaller watersheds where that capacity might be overwhelmed, and especially so if they drain directly into coastal areas. Overwhelming may occur when large inputs pass from the landscape to the stream or river, such as from sewage outfalls or agricultural runoff, or when flow rates are very high (Wollheim et al., 2018).

The health of our coastal estuaries and marshes, and their ability to provide all the services needed for a regenerative, diverse biosystem is directly tied to the health of the rivers, streams, ponds, wetlands, and groundwater upstream of them - and their ability to function as crucial sources of drinking water, habitat for fish and shellfish, wildlife, storm protection and more. Hydrology creates the interdependent connectivity of it all. We must recognize the connections and be aware we are always in a watershed. Our actions on the land have impacts downstream – and there is always a downstream - until we reach the ocean. Water has no choice but to flow downhill, and to carry along things it encounters. It is up to us to remove and stop our streams and rivers from encountering harmful things, and slowly degrading our coastal and marine systems. We do have a choice.

Here comes the good news!

When we give natural systems the time and space to function properly, they help us mitigate some of these inputs. We have already mentioned the contribution that beaver ponds can make. Similarly, riparian buffer zones between input sources and water bodies can be very beneficial. The latter can occur on scales from forest strips between agricultural fields and nearby streams, to vegetated areas between parking lots and drainage ditches, to sidewalk gardens and rain gardens in neighborhoods (Fig. 8), much like what is being proposed by the Emerald Web.

Figure 8. Sidewalk rain garden (Credit Catherine Neal https://extension.unh/resource/rain-gardens-design-and-installation)

And they make our open spaces more beautiful.

Figure 9. Rowley River, flowing through saltmarshes to Plum Island Sound and the Gulf of Maine. Photo c J.S. Aber, S.W. Aber, V. Valentine 2009.



Fazekas, H. M., McDowell, W. H., Shanley, J. B., & Wymore, A. S. (2021). Climate variability drives watersheds along a transporter-transformer continuum. Geophysical Research Letters, 48, e2021GL094050.

Pardo, L. H., Green, M. B., Bailey, S. W., McGuire, K. J., & McDowell, W. H. (2022). Identifying controls on nitrate sources and flowpaths in a forested catchment using a hydropedological framework. Journal of Geophysical Research: Biogeosciences, 127, e2020JG006140.

Ross, D. S., J. B. Shanley, J. L. Campbell, G. B. Lawrence, S. W. Bailey, G. E. Likens, B. C. Wemple, G. Fredriksen, and A. E. Jamison (2012), Spatial patterns of soil nitrification and nitrate export from forested headwaters in the northeastern United States, J. Geophys. Res., 117, G01009,

Whitney, C. Understanding the role of impoundments in river network-scale nitrogen exports in a dynamic landscape. PhD Dissertation, in prep., U. of New Hampshire.

Wollheim, W.M., Harms, T.K., Robison, A.L., Koenig, L.E., Helton, A.M., Song, C., Bowden, W.B. and

Finlay, J.C. (2022), Superlinear scaling of riverine biogeochemical function with watershed size. Nature communications, 13(1), pp.1-9.

Wollheim, W.M., Bernal, S., Burns, D.A., Czuba, J.A., Driscoll, C.T., et al. (2018), River network saturation concept: factors influencing the balance of biogeochemical supply and demand of river networks. Biogeochemistry 141, 503–521.


Jane Tucker

Jane grew up on the coast of North Carolina, and holds a B.S. and M.S. in Marine Sciences from UNC-Chapel Hill. Now living on the Massachusetts coast, she works at the Marine Biological Laboratory’s Ecosystems Center in Woods Hole. She is part of a team of scientists that studiesthe ecology and biogeochemistry ofthe marshes,estuaries, and watersheds inthe Plum Island EcosystemsLongTerm Ecological Research program and at other coastal sites. Her dry-land interests include gardening and dressage.

Wil Wollheim, Ph.D.

Dr. Wollheim is an Associate Professor in the Department of Natural Resources and the Environment at the University of New Hampshire, where he teaches courses on freshwater resources, aquatic ecosystems, and environmental modeling, and mentors many graduate students. He is also co-director of UNH’s Water Systems Analysis Group and leads the watershed research component of the Plum Island Ecosystems Long Term Ecological Research project. Wil’s research focuses on the physical, chemical, and biological processes that shape hydrological systems, with an emphasis on human impacts – like land use effects, dams and removal of dams, nutrient pollution, and climate change. Wil and his lab group combine field monitoring, experiments, sensor deployments, and modeling to understand hydrological and biogeochemical dynamics at scales ranging from individual ecosystems, to whole river systems, to the global systems of inland waters. Wil serves on technical advisory committees for Ipswich/Parker River, Great Bay, and Casco Bay.

Christopher Whitney

Chris is a PhD student in the Department of Natural Resources and the Environment at the University of New Hampshire. Chris’ research focuses on understanding nitrogen removal from river networks by ponds and wetlands, in particular by beaver ponds, which are increasing in the Northeast. He has developed a GIS technique to determine the abundance of beaver ponds in the Parker and Ipswich River (MA) watersheds and combined it with data from in situ water quality sensors and experimental approaches. Chris enjoys collaborative research as well as working with members of local communities, and mentoring undergraduate students: “ …helping to teach and inspire students in the sciences has been just as rewarding as the research I am performing here at UNH.”

Chris will graduate Summer 2022. The working title of his dissertation is “Understanding the role of impoundments in river network-scale nitrogen exports in a dynamic landscape”.

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