Habitat alteration, urbanization, industrialization, population growth, environmental pollution as well as degradation, deforestation, desertification, global worming as well as global cooling- these are few popularly known term in present world. In the north-east coast of India, there are three diversified estuary, i.e. Bhagirathi estuary of Bhagirathi-Hooghly river, Talsary estuary of Subarnarekha river, Bhitarkanika estuary of Mahanadi river. The catchment area, flow and volume of water, number of tributary and sub-tributary, source region, length of the river, shape and size of river valley, nature and volume of runoff, micro and macro landform are the key controlling factors of estuarine dynamics of these three rivers. As the factors may vary from one rive to another, so the estuarine water and sediment variety also differs in respect of time and place. The river Ganga is the prime and influential perennial river in India, which gives an integrated socio-economic platform and also makes a huge delta in estuary region as a continue manner. One of the largest settlements (built up area) and huge fertile agricultural lands are found along with the river valley. So the two major types of surface runoff, like agricultural runoff and household runoff are the main elements, which mixing up with the river. Besides that, different thermal power plant and heavy and light industries are built up along with the river for sufficient water availibity. These wastages also mixing up with this water. Subarnarekha valley is a mining based valley, where maximum mining based runoff water is mixed up with water. Different dams are built on this river, which is reduced the supply of fresh water. As a result of it, water salinity in estuary will increase. On the other hand, Mahanadi has a valley based on mining and mining based industry. So water quality also influenced by mining industry based run off. Presently river barrage also constructed on the Mahanadi river, which is the also causing factor of water salinity increases at Bhitarkanika region. This is also a causing factor of disturbance of local hydrological cycle. Apart from this, few reasons are directly operating to make an impact on fishery sector and its associated environments.