Coastal areas include highly complex ecosystems that encompass many different and productive resources worldwide. Although having such great importance, the lack of basic knowledge concerning the marine habitat distribution and biodiversity along the Turkish shoreline is an undeniable reality. In this study, seagrass beds in the bays along the Eastern Aegean Sea coast were located and mapped. Traditionally, sea-truth data used for satellite-image and other analysis are collected through direct observations requiring scuba divers or by aquatic video-camera observation. This study included a combination of acoustic technology, video recording and interpretation, geomorphological, oceanographic, and sedimentological evaluation in order to make significant contributions of current technology. The classification of the evaluated Subbottom Profiler (SBP) records exhibited their high discrimination capacity between different sea-bed features, making them appropriate for ground distinction. Linking of the SBP data sets to the Side Scan Sonar (SSS) records (object-based analysis) provide to full coverage, high resolution benthic habitat maps. For this purpose, Side Scan Sonar, 3.5/10 kHz Subbottom Profiler data were collected to a range of 50 m water depth, the data was recorded for a total 1600 km 2 coastal area that consists of approximately a total 3000 km long and 1km wide grid system for Edremit, Çandarlı, Gülbahçe, Ildır, Güllük and Gökova Bays. In the study area, it was determined that the seagrasses are under danger where high human influence is located. Dense distribution of invasive macroalgae (Caulerpa cylindracea, Stypopodium schimperi) were seen at the southern and northern part of the study area subjected to human activities.