The time series data consist of the trajectories for three sets of drifter deployments, released in July 2021. The drifters were deployed off the coast of the Maltese Islands and in the stretch between Malta and Linosa. These surveys were carried out as part of the WaterColours project which had the aim of using satellite observations to follow trends in surface Chlorophyll-a concentrations and total suspended matter (TSM). These parameters provide important water quality markers. This project was supported by the Malta Council for Science & Technology Space Research Fund (SRF2019).