A Manta trawl equipped with a 335 µm mesh size was deployed outside the vessel wake and towed at a speed of 2–3 knots (approximately 1.5 m/s) for 15 minutes at all super-stations, except under high-current conditions or when excessive floating debris was present. The net was used to collect neustonic material, including fish larvae and microplastics from surface waters. Fish larvae were carefully sorted from the samples, photographed for morphological documentation, and preserved in 96% ethanol for subsequent genetic analyses. The remaining bulk biological material after sorting was stored in methylated ethanol for further genetic processing. Microplastics were also extracted from the same Manta trawl samples. Particles were identified and counted under a stereomicroscope, photographed for documentation, and preserved in vials containing filtered freshwater for further analysis. This dataset therefore provides integrated observations of ichthyoplankton and microplastic distributions in surface waters, supporting ecological, genetic, and pollution-related studies in marine environments.