The intensive use of estuaries and coasts for navigation practices makes dredging operations necessary in many cases. In several ways dredging and the disposal of dredged material can interfere with the physicochemical characteristics of the environment and thus with the communities occurring. Environmental disturbances can be evaluated in a spatial-temporal context and include burial, turbidity increases, switches in sediment types, changes to the hydrodynamic characteristics and toxicological hazards. Different ecosystems are sensitive to different types of disturbances. When planning a dredging project it is important to evaluate whether the expected disturbances will have an impact on the ecosystem and the services provided by it. The effects caused by the project should be separated from the naturally occurring fluctuations. To estimate the risks involved, the system and its communities have to be evaluated previously to the works. When the abiotic parameters such as stream velocities and sediment types and the communities occurring in a system are identified, it is possible to estimate which species are at risk by the activities planned and to evaluate the major hazards depending on the sensitivity of the species and the properties of the system. These characteristics will also determine the recovery capacity after disturbance. Impact reduction is possible by the choice of dredging techniques and management strategies. These strategies include the selection of the best locations and timing of the works. In every environmental project, also social and economical aspects have to be taken into account, because the system involved has a lot of stakeholders, all with their own interests. The best option is aiming at multiple benefits of the project, creating win-win situations and satisfying several stakeholders.