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Geographically and geologically, the Danube comprises of three distinct sections: the upper, the middle, and the lower basins. All along its course, the landscape surrounding the river is physically very diverse: it ranges from mountainous terrain to wide floodplains, which also, as expected, results in a wide variation of climatic conditions.

Allocation of water resources, the variety of natural vegetation, and different agricultural uses all vary with the climate and different topology. Water resources are largely rationed in accordance to agriculture and other manufacturing activities. Given that the basin can grow specialized crops owing to its temperate climate, air and soil moisture, and the mineral contents, it is subjected to intense agricultural exploits but also frequent irrigation.

Water is supplied from the river, as well as from the rainfall, which can be inconsistent sometimes, resulting in seasonal droughts. This is one of the reasons why the pollution across the area is diffused, along with insufficient waste water treatment, all contributing to the changes in the river structure and morphology. The other is groundwater and soil pollution. Irrigation and waste water treatment contribute to the contamination of sediments and soils, which spread far and fast with the river.

During the summer, when water levels of the Danube are quite low, in the Upper Basin, the river is known to sink into a series of underground channels at various points of its course, what is known as Donauversickerung. Curiously, the word translates from German as the 'disappearance of Danube'. The stream does not seep through the soil, but smoothly flows through a sequence of underground craters. The stream reappears in the area further south of Aachtopf, north into Constance Lake, where it flows into the Rhine, thus linking the Black Sea with the Northern Sea.

The underground karst water system through which it flows has, over centuries, formed layers of limestone formations. The vast amounts of underground water flows through them it erodes the limestone.

As the erosion has moulded the upper Rhine valley, most Alpine streams directed their flow into the Rhine. For that reason, and due to limestone decay and the abrasion of the karst system, it is expected that the upper Danube flow may eventually collapse the sequence of caves and one day give way to the Rhine.

When the regions flood, extremely high concentration of suspended sediments are released from reservoirs causing severe implications for agriculture and forestry in the downstream sections that follow, in which thick layers of sediments get deposited.

Due to erosion and sedimentation processes cross sections of the river are subjected to major changes and may increase the flood risk. The remaining free flowing sections of the Danube can, thus, be impaired due to a deficiency of inflowing sediments, mainly coarse materials (the aforementioned debris) which tend to get trapped upstream and cause troubles further ahead if left unattended.

As a consequence, gradual degradation of the river bed will most likely happen, in some places reaching up to a few centimetres per year. This can lead to the decrease of water level at a similar rate and less frequent instances of flooding in those spots. In turn, the ecology of the flood plains, where the major relevant wetland areas are found, is changing slowly. Implications for the quantity and quality of water near wells have to be considered too.

The karst formations are located all over the Balkan peninsula, which has over centuries moulded the caves and underground drainage channels. Because of this there are large volumes of subsurface water and channels that have formed aquifers. The water from these formations along the Dinaride and Carpathian mountains drains into the Danube and downstream to the Black Sea. The water levels are, thus affected by the volume of streams, runoffs, precipitation, and snow and ice melting.

The recent sediment management strategies refer to dredging activities in fords and in harbour entries; in some sections like in Austria artificial feeding of the river bed with coarse material is applied to reduce further lowering of substructure. Both sets of activities are costly and may initiate impacts somewhere downstream.

The release of sediments from reservoirs during floods happens without a general pattern and largely uncontrollably. It can be concluded that there is no regional sediment management, it being based on individual and local actions and without any trans-boundary cooperation. One of the reasons can be the limited knowledge of the processes related to the interaction of water and sediments in the river and in the flood plain.

The main emphasis of analytical and methodological approaches is on the main stem of the Danube and the input from the major tributaries.

Changes in the river bed are classified according to aggradation, degradation, and the stabilization of highly dynamic river sections. Characterization of the flood plain area should provide information about the most influential factors for the sediment balance and sediment management, including trends in the sediment data related to human interventions in the basin.

There have been some evidences of changes to river structure and morphology due to damming. Hydro-morphological alterations and the management of infrastructure for energy, navigation, and flood defence, is a key issue that affects the ecological functioning of the Danube ecosystem. It impacts on sediment transport, longitudinal and lateral connectivity of the river, and has direct impact on the functioning of the Danube ecosystem and on related wetlands and floodplains.

Climate and human impact, including the increased damming of sections of the river has led to reduced river flow and terrestrial sediment input on the river flow and nutrient delivery to the wetlands.

And, finally, the Danube River Basin is an important breeding ground for species of flora and fauna, some that are unique to the area. They help regulate the activities of the basin by sustaining populations of living organisms, both in the river, the series of wetlands - which are particularly prolific - and the rest of the surrounding territories. The species include remarkable groups of insects, amphibians, fish, birds, and other animals, and abundant plants.

The region is an immensely valuable habitat, biologically, geophysically, and environmentally. Biodiversity efforts in the area continuously focus on its conservation and the reduction in disturbances or damages that would undermine the varieties and numbers of species in the ecosystem. Systems of research, monitoring, and protection are in place to evaluate and mitigate pressures on natural dynamics and uphold its principles.