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The world’s population increase in the last 50 years has affected water resources in several aspects. More water is now needed and therefore more wastewater is produced and discharged to other water bodies of the planet. These two aspects madewater a limited and strategic natural resource in terms of its quality and quantity. It is then easy to conclude that water, like all the limited and vulnerable resources, has become one of the potential targets of terrorists.

Numerous examples of response plans exist for natural emergencies, such as floods, hurricanes, fires, etc., in many areas of the world, as in the National Incident Management System in the United States which was developed so that responders from different jurisdictions and disciplines can work together to better respond to natural disasters and emergencies, and the Centre for Emergency Preparedness and Response (CEPR) in Canada (http://www. phac-aspc.gc.ca/cepr-cmiu/). Plans that handle industrial chemical disasters also have been developed, such as the Seveso Directive II (named after the Seveso accident in 1976). This was developed by the European Commission in discussions with representatives from EU Member States and is an EU Directive that serves to mitigate and minimize accidents, threats, and hazards from industrial accidents involving dangerous substances (http://www.cemac.org/english/E2009002.html).

The laws of nature are simple and objective: they work inevitably and do not depend on an observer. They will work exactly the same way, even if this observer never existed: they are just absolute truth. At present, we can say already, that the main lows drivingwater motion in large basins arewell known. However, it is still a very long and challengingway from a basic understanding to effective use of these laws in applications! Equations, written in order to express these laws for geophysical environment, are objective—but not at all absolute: they depend on observer (like equations of Eulerian/Lagrangian representation), on choosing an inertial/non-inertial system of coordinates, on our knowledge of the processes under description etc. Moreover, solutions of these equations for real basins are always difficult to obtain: first, because of the equations are complicated, second, because they are simply always incomplete! Indeed, even though the Laws are simple, they play in a very complicated environmental systems, so that we, objectively, can never take into account the processes involved; we principally cannot provide for a large geophysical system (like sea, lake or lagoon) , and initial and boundary conditions.

The hydrodynamic equations are a set of equations that describe themovement of a water body through a set of variables, the so-called state variables. The basic equations that govern the development of these variables can be derived in its full form through the application of conservation laws. In sea water 7 variables completely define the state of the fluid. These variables are the density ρ of the water, the three velocity components , , in the direction of , , , the pressure , the temperature and the salinity . If only fresh water systems are concerned, there is no salinity as a variable, reducing the number of state variables to 6.

Clear understanding that the human year-by-year negatively affects natural environment brings up the idea of sustainable development (WCED, 1987), which includes reduction of anthropogenic impact down to a level assimilated by nature. To implement the last one practically, permanent efforts on development and step-by-step implementation of “good” decisions are needed at the global and local scales. A process of elaboration of such a decisions includes several obligatory steps: gathering of data, extracting an information and its analysis against selected criteria, and, finally, development of decisions and implementation of them (Figure 1).

Water masses, dissolved substances and particulate matters in coastal lagoons are set and maintained in motion by hydrodynamic forces such as sea level oscillations at the inlet, buoyancy inputs from river discharge and heat fluxes at the surface, winds, atmospheric pressure, gravity and earth rotation. Considering a lagoon as an input–output system, these forces are the system’s inputs while the lagoon’s response is the system’s output. Given the physical nature of most forcing functions, it is customary to discuss oceanographic data analysis methods in terms of hydrodynamic variables such as sea levels, currents, etc, even though these methods apply equallywell to time series of other ecosystem variables such as sunlight, chlorophyll-a, nutrients, etc. In this context, the objective of time series analysis is to isolate and describe the variability of the output and attribute this variability to one or more of the forcing input functions.

Computational fluid dynamics is concerned with the numerical solution of the differential equations of fluid dynamics. The reason why this filed is so important is because there are only few examples of flows where we can find analytical solutions of the flow field. When applying these equations to real world examples we have the problem that the flows become extremely complex, impossible to be described by closed formulas.

Whenever policy decisions are to be made affecting the natural resource Water—arguably the most precious natural resource—an implacable scrutiny is to be expected. Legal demands are huge as the large number of EU directives targeting water testifies, from which stand out the Nitrates Directive, the Urban Wastewater Directive, the Drinking Water Directive, the Bathing Water Directive and the Water Framework Directive. Media and public opinion at large are continuously exerting a strong pressure over these policies. Decisions need to be thoroughly supported and documented and this is where computers come into play. Modelling tools, in the form of Decision Support Tools, are extensively used both to detect and select the “best” solution and to prove that the best solution was chosen.

The future long-term trend in science, education and management, emerged from the overall policy goal of building a knowledge-based society and sustainable development. To achieve this goal, a new, revolutionary, theoretical development is needed, which allows: (i) the identification and understanding of complex organization across space and time scales of the nature and society; and (ii) the ecosystem (holistic) approach and adaptive management of the environment, human societies and their co-development under the pressure of different driving forces. Among a wide range of drivers and pressures, special attention should be paid to potential social instability and unexpected human behavior (e.g., terrorist attack).

The aim of this paper is to contribute to the developments of environmental indicators, which are an indispensable tool for ecosystem health assessment and ecosystem-based management. Most decision makers request scientific advice to be given in the form of indicators.