Freshwater lakes in most inhabited areas of the world are threatened by water quality issues. Standard water conservation measures have shown efficiency in the past; however, polluted lakes have only partially recovered from eutrophication. Our knowledge is still incomplete about the sensitivity of these lakes to different anthropogenic sources and to the changes in their internal processes due to global warming. In this article, we present a database comprising sediment data from Lake Balaton (Hungary), which can facilitate further analysis helping to better understand the internal processes and changes occurring in the lake. The published dataset includes the following parameters measured in 4211 lake bed sediment samples: pHKCl, calcium carbonate (CaCO3), organic carbon (Corg), total nitrogen (Ntotal), soluble phosphorus (AL-P2O5) and soluble potassium (AL-K2O), magnesium (Mg2+), zinc (Zn2+), copper (Cu2+) and manganese (Mn2+). We are confident that our database serves as a strong basis for further research relating to freshwater lakes influenced by human activities.