The chronological information provided by sediment cores about the beginning and evolution of anthropogenic contaminants is crucial for understanding the influence of humans on the environment. The dataset provides information about the vertical distribution of heavy metals (HMs), metalloids and various organic contaminants (OCs) including contemporary contaminants of emerging concern (CECs), such as pharmaceuticals and personal care products (PPCPs) and pesticides; as well as persistent organic contaminants (POPs) such as polycyclic aromatic hydrocarbons (PAHs), perfluoroalkyl substances (PFASs), organophosphorus flame retardants (OPFRs) in sediment cores of two different sampling areas (North and South) of L'Albufera lake. Additional information about the 14 C-data of the organic matter present in the different layers of the sediment cores, and the 14 C-data of the seashells found in some of them are shown. The dataset includes physico-chemical analyses of sediment characteristics at the different selected depth levels such as Organic Carbon (C org ), Inorganic Carbon (IC), Total Nitrogen (TN), Total Sulphur (TS) and texture. Furthermore, ecological risk assessment of these contaminants in surface sediment layers is performed to ascertain is potential toxicity. These data supplement the findings presented and considered in the research article " Exploring Organic and Inorganic Contaminant Histories in Sediment Cores Across the Anthropocene: Accounting for Site/Area Dependent Factors" . Therefore, these data altogether are useful for researchers seeking to assess long-term impact of contamination., (© 2024 The Author(s).)