In this contribution, the diversity of coastal systems of the Eastern Aegean Sea coasts, their natural characteristics and dynamics, and the human presence are discussed, aiming at the formulation of an integrated management plan for human activities. The physiography of the coastal area is characterized by the alteration of peninsulas and gulf systems, the result of the geodynamics of the extended area, with the E-W main orientation. This diverse physiography of the Eastern Aegean coastal area formed an appropriate place for human inhabitation since the prehistoric periods. The human presence nowadays is related to activities, which act as pressures on the state of the Aegean Sea coastal area, having an impact on it. The activities are urbanization (domestication and tourism), agriculture, aquaculture, fishing, industry, and shipping. The human response is needed focused on the mentioned parameters. To propose a management plan for the Eastern Aegean Sea coastal system, the human activities, their pressures, and impacts on the state of the eight bay systems of the area are summarized, the state of the Eastern Aegean Sea marine environment is presented, and recommendations for a future integrated management plan are formulated.