Estuarine systems currently face increasing pressure due to population growth, rapid economic development, and the effect of climate change, which threatens the deterioration of their water quality. This study uses an open-source model of high transferability (Delft3D), to investigate the physics and water quality dynamics, spatial variability, and interrelation of two estuarine systems of the Portuguese west coast: Mondego Estuary and Óbidos Lagoon. In this context, the Delft3D was successfully implemented and validated for both systems through model-observation comparisons and further explored using realistically forced and process-oriented experiments. Model results show (1) high accuracy to predict the local hydrodynamics and fair accuracy to predict the transport and water quality of both systems; (2) the importance of the local geomorphology and estuary dimensions in the tidal propagation and asymmetry; (3) Mondego Estuary (except for the south arm) has a higher water volume exchange with the adjacent ocean when compared to Óbidos Lagoon, resulting from the highest fluvial discharge that contributes to a better water renewal; (4) the dissolved oxygen (DO) varies with water temperature and salinity differently for both systems. On the one hand, for Mondego Estuary during winter the DO levels mainly fluctuate with salinity. On the other hand, for Óbidos Lagoon, DO distribution is determined by both water temperature and salinity. During summer, the high residence time and water temperature limit the DO levels in both systems. The high transferability and superior stability of Delft3D make this model a foundation for realistic simulation and research of distinct estuarine systems, giving support to their maintenance and restoration.

Coastal floods are currently a strong threat to socioeconomic activities established on the margins of lagoons and estuaries, as well as to their ecological equilibrium, a situation that is expected to become even more worrying in the future in a climate change context. The Ria de Aveiro lagoon, located on the northwest coast of Portugal, is not an exception to these threats, especially considering the low topography of its margins which has led to several flood events in the past. The growing concerns with these regions stem from the mean sea level (MSL) rise induced by climate changes as well as the amplification of the impacts of storm surge events, which are predicted to increase in the future due to higher mean sea levels. Therefore, this study aims to evaluate the influence of MSL rise on the inundation of Ria de Aveiro habitats and to assess the changes in inundation patterns resulting from frequent storm surges (2-year return period) from the present to the future, assessing their ecological and socioeconomic impacts. For this, a numerical model (Delft3D), previously calibrated and validated, was used to simulate the lagoon hydrodynamics under different scenarios combining MSL rise and frequent storm surge events. The numerical results demonstrated that MSL rise can change the vertical zonation and threaten the local habitats. Many areas of the lagoon may change from supratidal/intertidal to intertidal/subtidal, with relevant consequences for local species. The increase in MSL expected for the end of the century could make the lagoon more vulnerable to the effect of frequent storm surges, harming mostly agricultural areas, causing great losses for this sector and for many communities who depend on it. These extreme events can also affect artificialized areas and, in some cases, endanger lives.

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Reliable predictions of future inundation extent within estuaries require a precise evaluation of future extreme sea levels and the application of accurate numerical models that account for the physical processes driving estuarine hydrodynamics. In this study, a methodology that integrates the estimation of local extreme sea levels with high-resolution numerical modeling was applied to assess the future inundation extent in five estuarine systems located on the Portuguese Coast. The main findings obtained were compared with available results from the popular bathtub approach, that disregards the physical processes driving estuarine hydrodynamics and therefore provide imprecise predictions of inundation extent and associated socio-economic impacts. The inundation extent is revealed to be highly dependent on the extreme sea levels and on the estuarine geomorphology, which controls the propagating long-wave. As the long-wave height is highly attenuated within estuaries that have adjacent low-lying areas, restricted inlets, or extensive tidal flats, the results of this study revealed that the extent of inundation is considerably smaller than that obtained by the bathtub approach. The uncertainties associated with mean sea level rise and the estuarine geomorphological evolution constitute the greatest difficulty in assessing the extent of flooding, posing major challenges to the efficient and sustainable management of estuaries.

The interaction between tide, river runoff, and wind in coastal lagoons induces complex salinity gradients, which are remarkable when the meteorological forcing is exacerbated. This work aims to characterize the salinity structure under extreme freshwater and wind events in the Ria de Aveiro coastal lagoon (Portugal). The Delft3D model was implemented and validated in 3D mode and used to perform simulations forced with extreme freshwater and wind scenarios. Results show that forcing conditions determine salinity stratification intensity and location. Generally, stratification increases as the freshwater increases, while the salinity intrusion moves downstream. Extreme wind tends to destroy stratification but fails to promote full-depth mixing, which is also dependent on the wind direction, as shown for the Espinheiro channel. The salinity intrusion is also impacted by wind events, being NW storms responsible for an upstream salt transport along the Mira channel and a downstream transport along the Espinheiro channel, and SW storms for an upstream displacement of the salinity intrusion along the São Jacinto channel. Finally, it is observed that the advection of a freshwater plume from the Vouga River into the middle of the São Jacinto channel under high freshwater scenarios causes an unusual local salinity pattern. This plume can either be pushed upstream or prevented from entering the channel, depending on the wind direction.