The East Java coast has biodiversity potential, including microalgae. Microalgae are primary producers for the aquatic ecosystem, whose distribution depends on water quality parameters and sub-habitat characteristics. The purpose of this study was to analyse and identify the microalgae, as well as environmental quality parameters based on sub-habitat characteristics in the northern part of the East Java coast, Indonesia. The research was conducted from March to June 2023. Sample sites were determined using purposive sampling techniques at nine sites located in Gresik, Lamongan, and Tuban coasts. Water samples were collected from various sub-habitats, including the water column, sediments, rocks, mangroves, artificial substrates, macroalgae, and water plants consisting of water hyacinth (Eichhornia crassipes) and Coontail (Ceratophyllum demersum). The obtained results depicted microalgae found were from Bacillariophyceae, Chlorophyceae, Chrysophyceae, Coscinodiscophyceae, Cyanophyceae, Dinophyceae, Trebouxiophyceae, and Zygnematophyceae. Bacillariophyceae dominated the community in all sites. The expected outcome of this study is to provide and complete the database of microalgae morphologically based on sub-habitat characteristics, particularly on the north coast of East Java, Indonesia.