This dataset contains the number and fork length of Aphanius fasciatus and Gambusia holbrooki individuals caught in traps within pools and channels in Akrotiri SBA, Cyprus between 26th February 2018 and 19th March 2019. Fish were collected from submerged and semi-submerged traps within six pools and three channels within the lake approximately every two weeks before being measured, sexed as obvious males and then released. Traps were deployed for 24 hours before data were collected. Water temperature, dissolved oxygen and conductivity were also measured. Data were collected as part of a Defra Darwin Initiative Plus project to ascertain baseline data on native and non-native fish populations in the Sovereign Base Area of Akrotiri. Full details about this dataset can be found at https://doi.org/10.5285/ad7068c3-5225-437a-ae58-8422cb7e3454