**2. Methods**

#### **2.1 Study site**

The Mondego river basin is located in the central region of Portugal. The drainage area is about 6670 km2 and the annual mean rainfall is between 1000 and 1200 mm. The area covered in this study refers to the whole Mondego estuary (Fig. 2), 32 km in length from its ocean boundary defined approximately 3 km outward from the mouth to Pereira bridge.

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

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

The Mondego river basin is located in the central region of Portugal. The drainage area is about 6670 km2 and the annual mean rainfall is between 1000 and 1200 mm. The area covered in this study refers to the whole Mondego estuary (Fig. 2), 32 km in length from its ocean boundary defined approximately 3 km outward from the mouth to Pereira bridge.

aquatic ecosystems with extensive intertidal areas (Duarte & Vieira, 2009b)

development.

**2. Methods 2.1 Study site** 

Fig. 2. Location and layout of river Mondego estuary

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

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 by the Murraceira Island (Fig. 3).

Fig. 3. Aerial views of Mondego estuarine main zone

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).

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

A Hydroinformatic Tool for Sustainable Estuarine Management 9

The Mondego River monthly inflows were calculated based on the analysis conducted for the daily average values measured at the Coimbra dam-bridge in the period 1990-2004 (Fig. 7).

Fig. 7. Average monthly flow observed at the Coimbra dam-bridge (1990-2004).

demand for existing intensive oriziculture activity in the Pranto river catchment.

Based on this available data, the typical dry-weather flow (corresponding to the 90% percentile on the cumulative flow rate curve) is about 15 m3.s-1, while the annual average flow value was 75 m3.s-1. The maximum flow value for sizing the minor bed of the main

The values that were estimated for the Pranto River inflow to the Mondego estuary south arm correspond to those observed during field work, considering the flow discharge curves

So, average daily values of 0 (closed sluices), 15 and 30 m3.s-1 were considered. They correspond, respectively, to discharges carried out during part of the tidal cycle and continuous discharges that are usual in periods of greater rainfall, considering the water

Fig. 6. Mondego estuary grain-size map

channel was estimated about 340 m3.s-1.

of the three Alvo sluices (Fig. 8).

For some decades, the river Mondego estuary was under severe ecological stress, mainly caused by eutrophication of its south arm due to the combination of the nutrient surplus with low hydrodynamics and high salinity, because, until the end of 1998, this sub-system was almost silted up in the upstream areas (Fig. 5), drastically reducing the Mondego river water inflow. Hence, the south arm estuary water circulation was mainly driven by tide and wind, originating, in dry-weather conditions, a coastal lagoon-like behaviour. The freshwater inflow was seasonal and only provided by the (small) discharges of the Pranto River, a tributary artificially controlled by the *Alvo* sluices, located 1 km upstream from its mouth.

The most visible effect of this important hydrodynamic constrain was the occurrence of episodic macroalgae blooms and the concomitant severe decrease of the area occupied by *Zostera noltii* beds. So, for the control of this eutrophication process, it became crucial to obtain field data to characterize the real trophic status of this aquatic ecosystem, as well as to better understand the major mechanisms that regulate the abundance of opportunistic macroalgae in order to eradicate its periodic early spring algal blooms.

Fig. 5. Silting up process occurred in the upstream areas of the estuary south arm

Figure 6 shows the size-grain distribution of the sediments in the Mondego estuary main zone (Cunha & Dinis, 2002). A strong correlation was found with the flow channels configuration that occurs during low tide. This information could be very useful for the roughness coefficient definition along the estuarine system, considering or not the variability of the bottom shear stress.

For some decades, the river Mondego estuary was under severe ecological stress, mainly caused by eutrophication of its south arm due to the combination of the nutrient surplus with low hydrodynamics and high salinity, because, until the end of 1998, this sub-system was almost silted up in the upstream areas (Fig. 5), drastically reducing the Mondego river water inflow. Hence, the south arm estuary water circulation was mainly driven by tide and wind, originating, in dry-weather conditions, a coastal lagoon-like behaviour. The freshwater inflow was seasonal and only provided by the (small) discharges of the Pranto River, a tributary artificially controlled by the *Alvo* sluices, located 1 km upstream from its

The most visible effect of this important hydrodynamic constrain was the occurrence of episodic macroalgae blooms and the concomitant severe decrease of the area occupied by *Zostera noltii* beds. So, for the control of this eutrophication process, it became crucial to obtain field data to characterize the real trophic status of this aquatic ecosystem, as well as to better understand the major mechanisms that regulate the abundance of opportunistic

macroalgae in order to eradicate its periodic early spring algal blooms.

Fig. 5. Silting up process occurred in the upstream areas of the estuary south arm

variability of the bottom shear stress.

Figure 6 shows the size-grain distribution of the sediments in the Mondego estuary main zone (Cunha & Dinis, 2002). A strong correlation was found with the flow channels configuration that occurs during low tide. This information could be very useful for the roughness coefficient definition along the estuarine system, considering or not the

mouth.

Fig. 6. Mondego estuary grain-size map

The Mondego River monthly inflows were calculated based on the analysis conducted for the daily average values measured at the Coimbra dam-bridge in the period 1990-2004 (Fig. 7).

Fig. 7. Average monthly flow observed at the Coimbra dam-bridge (1990-2004).

Based on this available data, the typical dry-weather flow (corresponding to the 90% percentile on the cumulative flow rate curve) is about 15 m3.s-1, while the annual average flow value was 75 m3.s-1. The maximum flow value for sizing the minor bed of the main channel was estimated about 340 m3.s-1.

The values that were estimated for the Pranto River inflow to the Mondego estuary south arm correspond to those observed during field work, considering the flow discharge curves of the three Alvo sluices (Fig. 8).

So, average daily values of 0 (closed sluices), 15 and 30 m3.s-1 were considered. They correspond, respectively, to discharges carried out during part of the tidal cycle and continuous discharges that are usual in periods of greater rainfall, considering the water demand for existing intensive oriziculture activity in the Pranto river catchment.

A Hydroinformatic Tool for Sustainable Estuarine Management 11

monitoring stations at Mondego estuary south arm were selected in order to represent the different flow regimes observed in this system. Water level, velocity, salinity, temperature and dissolved oxygen were measured in situ and water samples were collected for physical

Dissolved fraction seems to be the most representative of nutrients transport inside the south arm of this estuary, followed by the suspended particulate matter fraction. This finding was very relevant to understand the high eutrophication vulnerability of this subsystem, since these fractions represent the nutrients immediately accessible to the

An example of the sampling programme results is depicted in Figure 10 showing the average monthly values of salinity obtained (in 2000-2001) at Lota station (S1) and Pranto

and chemical system characterization.

**2.3 Dye tracer experiments** 

ecosystems protection must be considered.

and mining activities or road-river accidents.

macroalgae tissues incorporation on the growing process.

river mouth station (S3), as well as its variation over a medium tidal cycle.

Fig. 10. Average salinity variation in the Mondego estuary south arm (2000-01)

The sampling data analysis was crucial to better understand eutrophication mechanisms and allowed us to conclude that the occurrence of green macroalgae blooms is strongly dependent on the estuarine flushing conditions, salinity gradients and nutrient loading characteristics, availability and residence time (Martins et al., 2001; Duarte et al., 2002).

Hydrodynamics and pollutant discharge dispersion characteristics are determinant factors in river basin planning and management, where different waters uses and aquatic

Net advection and longitudinal dispersion play important roles in determining transport and mixing of substances and pollutants discharged into the aquatic systems. In order to enhance water sources protection, the knowledge of transport processes is of increasing importance concerning the prediction of the pollutant concentration distribution, particularly when resulting from a continuous or accidental spill event caused by industrial

Generally, there are two approaches to calculate the transport of solutes in water bodies. One is the more classical calculation based on exact river morphological and hydraulic input

Fig. 8. Pranto river annual (1993-94) flow discharge into the Mondego estuary south arm

In this study, the tidal harmonic signal at Figueira da Foz harbour was generated, for each simulated period, using the programme SR95 (JPL, 1996). Fig. 9 presents an example of a monthly tidal signal used in the *Mondest* model as a downstream boundary condition, during its calibration procedure (Duarte, 2005).

Fig. 9. Monthly tidal harmonic signal at Figueira da Foz harbour using the SR95 programme

#### **2.2 Sampling programme**

An extensive sampling programme was carried out during last two decades at three benthic stations. The choice of benthic stations was related with the observation of an eutrophication gradient in the south arm of the estuary, involving the replacement of eelgrass, *Zostera noltii* by opportunistic green macroalgae such *as Enteromorpha spp*. and *Ulva spp.*

Water column monitoring was performed by specific sampling campaigns, some of them in simultaneous with the benthic ones, at three other sites: Pranto river mouth (S3); *Armazéns* channel mouth (S2); and Lota (S1), downstream the *Gala* bridge). The location of water

Fig. 8. Pranto river annual (1993-94) flow discharge into the Mondego estuary south arm

during its calibration procedure (Duarte, 2005).

**2.2 Sampling programme** 

In this study, the tidal harmonic signal at Figueira da Foz harbour was generated, for each simulated period, using the programme SR95 (JPL, 1996). Fig. 9 presents an example of a monthly tidal signal used in the *Mondest* model as a downstream boundary condition,

Fig. 9. Monthly tidal harmonic signal at Figueira da Foz harbour using the SR95 programme

An extensive sampling programme was carried out during last two decades at three benthic stations. The choice of benthic stations was related with the observation of an eutrophication gradient in the south arm of the estuary, involving the replacement of eelgrass, *Zostera noltii* by

Water column monitoring was performed by specific sampling campaigns, some of them in simultaneous with the benthic ones, at three other sites: Pranto river mouth (S3); *Armazéns* channel mouth (S2); and Lota (S1), downstream the *Gala* bridge). The location of water

opportunistic green macroalgae such *as Enteromorpha spp*. and *Ulva spp.*

monitoring stations at Mondego estuary south arm were selected in order to represent the different flow regimes observed in this system. Water level, velocity, salinity, temperature and dissolved oxygen were measured in situ and water samples were collected for physical and chemical system characterization.

Dissolved fraction seems to be the most representative of nutrients transport inside the south arm of this estuary, followed by the suspended particulate matter fraction. This finding was very relevant to understand the high eutrophication vulnerability of this subsystem, since these fractions represent the nutrients immediately accessible to the macroalgae tissues incorporation on the growing process.

An example of the sampling programme results is depicted in Figure 10 showing the average monthly values of salinity obtained (in 2000-2001) at Lota station (S1) and Pranto river mouth station (S3), as well as its variation over a medium tidal cycle.

Fig. 10. Average salinity variation in the Mondego estuary south arm (2000-01)

The sampling data analysis was crucial to better understand eutrophication mechanisms and allowed us to conclude that the occurrence of green macroalgae blooms is strongly dependent on the estuarine flushing conditions, salinity gradients and nutrient loading characteristics, availability and residence time (Martins et al., 2001; Duarte et al., 2002).
