This chapter presents the role and importance of aquatic ecosystems for the functioning of the biosphere and as a strategic factor of human existence and civilization development. Aquatic ecosystems are presented as techno-ecosystems, the number and scale of which are increasingly expanding and acquiring the features of a global system, which includes various technical objects that interact with both nature, biosphere, and society. Effective management of these systems is the basis for harmonizing human relations with the planet’s biosphere. This chapter presents the major challenges in water resources management: increased water demand, deterioration of underground and surface water quality; disproportionality of water consumption in closely interconnected strategic sectors of the economy—water-food-energy; ineffective management of water and hydraulic infrastructure; water conflicts and climate change impact.