Salt is included in a variety of foodstuffs consumed by humans and since salt is contaminated with microplastics (MPs) causes health risk for humans. MPs can absorb pollutants that may transfer through organisms after the ingestion of MPs and affect the health of the human body by constantly taking the contaminated salt through food. Therefore, studies are needed to analyze the presence of MPs in salt pans. The present study was undertaken to investigate the spatiotemporal variations in the occurrence, distribution, and characterization of microplastics in water, sediment, and salt from salt pans of the Thoothukudi coastal region (October 2020–September 2021). Samples were collected from three sampling sites, viz., Tharuvaikulam (station 1), Thoothukudi (station 2), and Pazhayakayal (station 3) for analysis of the MPs throughout the year as they vary with season by Nile red staining method. The maximum occurrence of MPs in the salt was recorded as 52 MPs/kg during the monsoon season, in sediments it was 45 MPs/kg post southwest monsoon season, and in surface water samples it was 42 MPs/liter post southwest monsoon season at station 1. The dominant size of MPs for all the three samples was <0.5 mm post southwest monsoon season. White color with irregular-shaped MPs was found to be dominant throughout the study. The predominant composition of the extracted MPs was characterized by Fourier transform infrared spectroscopy and identified as polyethylene and polypropylene in all the samples. Display omitted •Spatiotemporal variations of MPs were analyzed in the salt pans.•The dominant size recorded was — <0.5 mm, shape — fragment and irregular, color — white, and polymer — PE & PP.•High level of MPs was found in salt during monsoon season at Station 1 due to wind velocity and anthropogenic activity.•The outcome of this study creates awareness among people to reduce MPs pollution.