Understanding estuarine characteristics is crucial for managing aquatic ecosystem and aquaculture. A delta is a dynamic area that influence by both sea and river. Research on a micro-tidal estuary remains limited, particularly in Indonesia. To understand the estuarine management in the delta, this research provides an overview about the hydrological characteristics in Wulan Delta Estuary. This research is important to maintain agriculture, aquaculture, and mangrove ecosystem. Morphological data and hydrological were collected in wet season and dry season. The tidal data were collected from 2007–2016. As the results, the river is predominant in the mixing process in the wet season and the tides in the dry season. A low mixing energy causes stratification in the water column, particularly in a depth water depth. In a shallow water depth, salinity circulation is homogenous. In dry season, the sea water can penetrate into the river up to more than 5 km, due to smooth river bed that may harm the agricultural area in surrounding.