Ponds are widespread yet highly vulnerable freshwater habitats that support diverse aquatic and terrestrial plant communities influenced by land use and water characteristics. The PONDY (Pond vegetation data and water physico-chemical parameters) dataset integrates vegetation and water physico-chemical data that have been collected to understand the responses of vegetation to environmental parameters. The dataset comprises 575 plots, of which 232 are aquatic and 343 are terrestrial, derived from 115 ponds across continental and insular areas of Italy. The dataset includes 743 vascular plant taxa and 5 macroalgae encompassing 364 genera and 89 families. Terrestrial plots host 690 taxa belonging to 87 families, while aquatic plots host 117 taxa belonging to 36 families. The dataset includes 10 taxa belonging to the Italian Red List and 39 alien species. Moreover, 11% of the aquatic plots have been classified in a Habitats Directive 92/43/EEC habitat type, while 48% have been classified in a EUNIS habitat type. The dataset contains, for each plot, measurements of physico-chemical water variables such as dissolved oxygen, water depth, and temperature, pH, turbidity, conductivity, and nutrient concentration. The PONDY dataset provides comprehensive information on plant diversity and abundance, community composition, habitat types, and water chemistry in Italian ponds, serving as a key resource for studying plant–environment relationships, developing predictive models, and supporting freshwater conservation efforts.