The dataset includes all the microplastics analysed for the manuscript "River–Groundwater Interaction and Recharge Effects on Microplastics Contamination of Groundwater in Confined Alluvial Aquifers" by Edoardo Severini, Laura Ducci, Alessandra Sutti, Stuart Robottom, Sandro Sutti and Fulvio Celico (https://doi.org/10.3390/w14121913). The dataset "MP (ctrl and sample).txt" contains the raw data of environmental and ctrl samples. The values of the ctrl samples were used to analyse the statistical differences between ctrl and environmental samples and subsequently used to define the identification parameters (threshold) for the microplastics identification in surface water and groundwater, contained in the file "MP (after ctrl sample).txt".