**1. Introduction**

Hydrodynamics and pollutant loads dispersion characteristics are determinant factors for an integrated river basin management, where different waters uses and aquatic ecosystems protection must be considered. Strategic Environmental Assessment (SEA) of river basin planning process is crucial to promote a sustainable development. Towards this purpose, the European Water Framework Directive (WFD) establishes a scheduled strategy to reach good ecological status and chemical quality for all European water bodies.

As transitional aquatic environments, where fresh and marine waters meet, estuaries are generally characterized by complex interactions, with strong gradients and discontinuities, between physical, chemical and biological processes. This complexity is often increased by intensive anthropogenic inputs (nutrients and pollutants) from urban, agricultural and industrial effluents, leading to sensitive structural changes (Paerl, 2006) that modify both the trophic state and the health of the whole estuarine ecosystem. As a response to this, there has been an enormous increase in restoration plans for reversing habitat degradation, based on knowledge of the processes which led to the observed ecological changes (Valiela et. al., 1997).

Estuaries are recognised worldwide for providing essential ecological functions (fish nursery, decomposition, nutrient cycling, and shoreline protection) and support multiple human activities (fisheries resources, harbours, and recreational purposes). Each estuary is unique, because of its specific geological structure, morphology, hydrodynamics, land use, and the inflowing freshwater´s characteristics (amount and quality).

Estuarine waters are generally characterized by intense biogeochemical processes that can renew the aquatic compartment, but their flushing capacity is mainly dependent on the hydrodynamic processes. The major driving forces of estuarine circulation are tides, wind, freshwater inflow, and general morphology (bathymetry, intertidal areas extension, roughness). The mixing and dispersion processes are critically dependent upon the salinity intrusion type (concerning it spatial distribution), which defines estuaries ranging from those with a highly stratified salt-wedge and a sharp halocline in the vertical structure to well-mixed systems.

The description of the estuarine transport process can be expressed by the definition of a transport time scale. This time scale is generally shorter than the time scale of the biogeochemical renewal processes and gives an estimate of the water-mass retention within the river basin system. So, the influence of hydrodynamics must not be neglected on

A Hydroinformatic Tool for Sustainable Estuarine Management 5

and hydrodynamics, mostly induced by the tidal range variability. It should be noted that the Lagrangian technique used for water transport time computation neglects the return flow effect at the estuarine mouth, which does not happen with the Eulerian approach. So, from a hydrological analysis in order to understand the flushing capacity of a tidal embayment, the Eulerian transport time scale seems to be the most representative parameter of all the processes occurring in the basin (Cucco et. al., 2009) and, being less dependent of tide variability, is able to describe the long term flushing dynamics of an estuarine system. A numerical modelling study applied to Tampa Bay (Florida) was performed comparing the residence times by this two different methods: Eulerian concentration based, and Lagrangian particle tracking. The results obtained with the Lagrangian approach showed a doubling of overall residence time and strong spatial gradients in residence time values

Since the lower WRT values can increase the estuarine eutrophication processes, an enhanced Eulerian approach was adopted in this research study, conceptualising the residence time (RT) as a characteristic of water constituents, also including the no conservative substances. Thus, RT values were calculated, for each location and instant, as an interval of time that is necessary for that corresponding initial mass to reduce to a predefined percentage of that value, using the developed *TemResid* module (Duarte, 2005). In this work, a value of 10% was defined for the residual concentration of the substance, attending to the fact that the effect of the re-entry of the mass in the estuary during tidal

Mathematical models are well known as useful tools for water management practices. They can be applied to solve or understand either simple water quality problems or complex water management problems of estuaries, trans-boundary rivers or multiple-purpose and stratified reservoirs. Accidental spills of pollutants are of general concern and could be harmful to water users along the river basins, becoming crucial to get knowledge of the

In this context, the mathematical modelling of dispersion phenomena can play an important role. Additionally, a craterous selection of mathematical models for application in a specific river basin management plan can mitigate prediction uncertainty. Therefore, intervention measures and times will be established with better reliability and alarm systems could efficiently protect the aquatic ecosystems, the water uses and the public health (Duarte & Boaventura, 2008). The benefits of the synergy between modelling and monitoring are often mentioned by several authors and the linkage of both approaches makes possible to apply cost-benefit measures (Harremoës & Madsen, 1999). Therefore, it is essential to correlate monitoring and modelling information with a continuous feedback, in order to optimize

An integrated approach (hydrodynamics and water quality issues) is fundamental to prioritise risk reduction options in order to protect water sources and to get a high quality of the raw material for the water supply systems (Vieira et. al., 1999). Moreover, integrated models allow the optimization of the designed monitoring network (Fig. 1, adopted from Stamou et. al., 2007), based on hydrodynamic and water quality parameters calculation at any section using data from a monitoring programme (necessarily applied to limited

The analysis of water column and benthos field data observed in the Mondego estuary (Portugal), over the last two decades, allowed us to conclude that hydrodynamics was a major factor controlling the occurrence of macroalgae blooms, as determinant of nutrients

both processes, the monitoring network and the simulation scenarios formulation.

flooding is considered (a significant effect for dry-weather river flow rates).

(Burwell, 2001).

dispersive behaviour of such pollutants.

number of sampling or measuring stations).

estuarine eutrophication vulnerability assessment, because flushing time is determinant for the transport capacity and the permanence of substances, like pollutants or nutrients, inside an estuary (Duarte, 2005).

Excessive nutrient input, associated with high residence times, leads to eutrophication of estuarine waters and habitat degradation. It is widely recognized as a major worldwide threat, originating sensitive structural changes in estuarine ecosystems due to strong stimulation of opportunistic macroalgae growth, with the consequent occurrence of algal blooms (Pardal et al., 2004).

Much progress has been made in understanding eutrophication processes and in constructing modelling frameworks useful for predicting the effectiveness of nutrient reduction strategies (Thomann & Linker, 1998) and the increase of the estuarine flushing capacity in order to reverse habitat degradation, based on knowledge of the major processes that drive the observed ecological changes (Duarte et. al., 2001).

Residence time (RT) is a concept related with the water constituents (conservatives or not) permanence inside an aquatic system. Therefore, it could be a key-parameter towards the sustainable management of estuarine systems, because its values can represent the time scale of physical transport and processes, and are often used for comparison with time scales of biogeochemical processes, like primary production rate (Dettmann, 2001). In fact, estuaries with nutrients residence time values shorter than the algal cells doubling time will inhibit algae blooms occurrence (Duarte & Vieira, 2009a).

Estuarine water retention (or residence) time (WRT) has a strong spatial and temporal variability, which is accentuated by exchanges between the estuary and the coastal ocean due to chaotic stirring at the mouth (Duarte et. al., 2002). So, the concept of a single WRT value per estuary, while convenient from both ecological and engineering viewpoints, is shown to be an oversimplification (Oliveira & Baptista, 1997). The WRT (so called as transport time scale) has been assessed by many authors to be a fundamental parameter for the understanding of the ecological dynamics that interest estuarine and lagoon environments (Monsen et al., 2002).

The WRT variability within the basin has been related, in many research works, with the variability of some important environmental variables (dissolved nutrient concentrations, mineralization rate of organic matter, primary production rate, and dissolved organic carbon concentration). In literature, the WRT is defined through many different concepts: age, flushing time, residence time, transit time and turn-over time. Nevertheless, the definitions of these concepts are often not uniquely defined and generally confusing.

WRT estimation can be done considering an Eulerian or a Lagrangian approach. In the first option, WRT is identified as the time required for the total mass of a conservative tracer originally within the whole or a segment of the water body to be reduce to a factor "1/e" (Sanford et al., 1992; Luketina, 1998, Wang et al., 2004; Rueda & Moreno-Ostos, 2006; Cucco & Umgiesser, 2006), being a property of a specific location within the water body that is flushed by the hydrodynamic processes. In the second one, it is identified as the water transit time that corresponds to the time it takes for any water particles of the sample to leave the lagoon through its outlet (Dronkers & Zimmerman, 1982; Marinov & Norro, 2006; Bendoricchio, 2006), being a property of the water parcel that is carried within and out of the basin by the hydrodynamic processes.

The two methods give similar results for transport time scales calculation only when applied to simple cases, such as regular basins or artificial channels (Takeoka, 1984). However, sensitive differences arise in applications to basins characterized by complex morphology

estuarine eutrophication vulnerability assessment, because flushing time is determinant for the transport capacity and the permanence of substances, like pollutants or nutrients, inside

Excessive nutrient input, associated with high residence times, leads to eutrophication of estuarine waters and habitat degradation. It is widely recognized as a major worldwide threat, originating sensitive structural changes in estuarine ecosystems due to strong stimulation of opportunistic macroalgae growth, with the consequent occurrence of algal

Much progress has been made in understanding eutrophication processes and in constructing modelling frameworks useful for predicting the effectiveness of nutrient reduction strategies (Thomann & Linker, 1998) and the increase of the estuarine flushing capacity in order to reverse habitat degradation, based on knowledge of the major processes

Residence time (RT) is a concept related with the water constituents (conservatives or not) permanence inside an aquatic system. Therefore, it could be a key-parameter towards the sustainable management of estuarine systems, because its values can represent the time scale of physical transport and processes, and are often used for comparison with time scales of biogeochemical processes, like primary production rate (Dettmann, 2001). In fact, estuaries with nutrients residence time values shorter than the algal cells doubling time will

Estuarine water retention (or residence) time (WRT) has a strong spatial and temporal variability, which is accentuated by exchanges between the estuary and the coastal ocean due to chaotic stirring at the mouth (Duarte et. al., 2002). So, the concept of a single WRT value per estuary, while convenient from both ecological and engineering viewpoints, is shown to be an oversimplification (Oliveira & Baptista, 1997). The WRT (so called as transport time scale) has been assessed by many authors to be a fundamental parameter for the understanding of the ecological dynamics that interest estuarine and lagoon

The WRT variability within the basin has been related, in many research works, with the variability of some important environmental variables (dissolved nutrient concentrations, mineralization rate of organic matter, primary production rate, and dissolved organic carbon concentration). In literature, the WRT is defined through many different concepts: age, flushing time, residence time, transit time and turn-over time. Nevertheless, the

WRT estimation can be done considering an Eulerian or a Lagrangian approach. In the first option, WRT is identified as the time required for the total mass of a conservative tracer originally within the whole or a segment of the water body to be reduce to a factor "1/e" (Sanford et al., 1992; Luketina, 1998, Wang et al., 2004; Rueda & Moreno-Ostos, 2006; Cucco & Umgiesser, 2006), being a property of a specific location within the water body that is flushed by the hydrodynamic processes. In the second one, it is identified as the water transit time that corresponds to the time it takes for any water particles of the sample to leave the lagoon through its outlet (Dronkers & Zimmerman, 1982; Marinov & Norro, 2006; Bendoricchio, 2006), being a property of the water parcel that is carried within and out of the

The two methods give similar results for transport time scales calculation only when applied to simple cases, such as regular basins or artificial channels (Takeoka, 1984). However, sensitive differences arise in applications to basins characterized by complex morphology

definitions of these concepts are often not uniquely defined and generally confusing.

that drive the observed ecological changes (Duarte et. al., 2001).

inhibit algae blooms occurrence (Duarte & Vieira, 2009a).

environments (Monsen et al., 2002).

basin by the hydrodynamic processes.

an estuary (Duarte, 2005).

blooms (Pardal et al., 2004).

and hydrodynamics, mostly induced by the tidal range variability. It should be noted that the Lagrangian technique used for water transport time computation neglects the return flow effect at the estuarine mouth, which does not happen with the Eulerian approach. So, from a hydrological analysis in order to understand the flushing capacity of a tidal embayment, the Eulerian transport time scale seems to be the most representative parameter of all the processes occurring in the basin (Cucco et. al., 2009) and, being less dependent of tide variability, is able to describe the long term flushing dynamics of an estuarine system.

A numerical modelling study applied to Tampa Bay (Florida) was performed comparing the residence times by this two different methods: Eulerian concentration based, and Lagrangian particle tracking. The results obtained with the Lagrangian approach showed a doubling of overall residence time and strong spatial gradients in residence time values (Burwell, 2001).

Since the lower WRT values can increase the estuarine eutrophication processes, an enhanced Eulerian approach was adopted in this research study, conceptualising the residence time (RT) as a characteristic of water constituents, also including the no conservative substances. Thus, RT values were calculated, for each location and instant, as an interval of time that is necessary for that corresponding initial mass to reduce to a predefined percentage of that value, using the developed *TemResid* module (Duarte, 2005). In this work, a value of 10% was defined for the residual concentration of the substance, attending to the fact that the effect of the re-entry of the mass in the estuary during tidal flooding is considered (a significant effect for dry-weather river flow rates).

Mathematical models are well known as useful tools for water management practices. They can be applied to solve or understand either simple water quality problems or complex water management problems of estuaries, trans-boundary rivers or multiple-purpose and stratified reservoirs. Accidental spills of pollutants are of general concern and could be harmful to water users along the river basins, becoming crucial to get knowledge of the dispersive behaviour of such pollutants.

In this context, the mathematical modelling of dispersion phenomena can play an important role. Additionally, a craterous selection of mathematical models for application in a specific river basin management plan can mitigate prediction uncertainty. Therefore, intervention measures and times will be established with better reliability and alarm systems could efficiently protect the aquatic ecosystems, the water uses and the public health (Duarte & Boaventura, 2008). The benefits of the synergy between modelling and monitoring are often mentioned by several authors and the linkage of both approaches makes possible to apply cost-benefit measures (Harremoës & Madsen, 1999). Therefore, it is essential to correlate monitoring and modelling information with a continuous feedback, in order to optimize both processes, the monitoring network and the simulation scenarios formulation.

An integrated approach (hydrodynamics and water quality issues) is fundamental to prioritise risk reduction options in order to protect water sources and to get a high quality of the raw material for the water supply systems (Vieira et. al., 1999). Moreover, integrated models allow the optimization of the designed monitoring network (Fig. 1, adopted from Stamou et. al., 2007), based on hydrodynamic and water quality parameters calculation at any section using data from a monitoring programme (necessarily applied to limited number of sampling or measuring stations).

The analysis of water column and benthos field data observed in the Mondego estuary (Portugal), over the last two decades, allowed us to conclude that hydrodynamics was a major factor controlling the occurrence of macroalgae blooms, as determinant of nutrients

A Hydroinformatic Tool for Sustainable Estuarine Management 7

This complex and sensitive ecosystem was under severe environmental stress due to human activities: industries, aquaculture farms and nutrients discharge from agricultural lands of

The Mondego estuary main zone (40º08'N 8º50'W), with only about 10 km long, is divided into two arms (north and south) with very different hydrological characteristics, separated

> **PRANTO RIVER**

The north arm is deeper and receives the majority of freshwater input (from Mondego River), while the south arm of this estuary is shallower (2 to 4 m deep, during high tide) and presents an extensive intertidal zone covering almost 75% of its total area during the ebb tide. The irregularity of its morphology and bathymetry is depicted in Fig. 4 (Duarte, 2005).

**SOUTH ARM ARM**

**MONDEGO RIVER**

**ATLANTIC OCEAN** 

**MURRACEIRA ISLAND**

**GALA BRIDGE** 

**NORTH ARM**

Fig. 2. Location and layout of river Mondego estuary

Fig. 3. Aerial views of Mondego estuarine main zone

Fig. 4. The Mondego estuary (main zone) bathymetry

low river Mondego valley.

by the Murraceira Island (Fig. 3).

availability and uptake conditions (Martins et al., 2001). Thus, the development of hydrodynamic (transport) processes characterization was obviously pertinent and useful.

Fig. 1. Interaction between monitoring and modelling for monitoring network optimization

The aims of this chapter are to present the structure of a hydroinformatic tool developed for the Mondego estuary − named *MONDEST model* − linking hydrodynamics, water quality and residence time calculation modules, in order to simulate estuarine hydrodynamic behaviour, salinity and residence times spatial distributions, at different simulated management scenarios. Model calibration and validation was performed using field data obtained from the sampling carried out over the past two decades (Duarte, 2005).The results of the model simulations, considering different river water flow scenarios, illustrate the strong asymmetry of flood and ebb duration time at the inner sections of this estuary, a keyparameter for a correct tidal flow estimation, as the major driving force of the southern arm flushing capacity. The saline wedge propagation into the estuary and the spatial variation of residence time values are also assessed under different management scenarios. The RT values obtained show a strong spatial and temporal variability, as expected in complex aquatic ecosystems with extensive intertidal areas (Duarte & Vieira, 2009b)

The conclusion of this chapter will confirm the crucial influence of hydrodynamics on estuarine water quality status (chemical and ecological) and the usefulness of this hydroinformatic tool as contribution to support better management practices and measures of this complex aquatic ecosystem, like nutrient loads reduction or dislocation and hydrodynamic circulation improvement, in order to contribute for a true sustainable development.
