Marine fish, algae and invertebrate invasive alien species (IAS) data from Akrotiri and Dhekelia, Cyprus. Data were collected during an 19-month monitoring period starting in February 2017 and ending in September 2018. Sampling occurred seasonally, approximately once every 3 months, and used an underwater visual census (UVC) method. The UVC involved divers swimming at a steady pace along three 25m transects, with each transect separated by a 5m gap. The transects were randomly placed, covering a variety of habitats such as seagrass beds and rocky habitats where possible. Fish species were recorded and abundance estimated within 2.5m on each side of the transect. Benthic species (algae and invertebrates) were recorded from quadrats placed every 1m along each 25m transect. Sampling carried out by the University of Cyprus and volunteer divers from the Western Sovereign Base Area Sub Aqua Club as part of a Defra Darwin Initiative Plus project to ascertain baseline data on native and non-native marine species in the Sovereign Base Area of Akrotiri. Full details about this dataset can be found at https://doi.org/10.5285/519d42bf-51cc-42a4-8673-5f2044cfa19a