Lake Pamvotis is a shallow Mediterranean lake located in northwestern Greece that has been recognized as an internationally important conservation site. Here, an unprecedented investigation was undertaken to obtain and evaluate data related to sedimentary organic matter, hydrocarbon content, and stable isotopes of Lake Pamvotis sediments, thus tracking the origin of organic inputs and providing a record of environmental status. The study revealed a distinct spatial distribution of polycyclic aromatic hydrocarbons (PAHs) with values between 34.7 and 1600 microg/kg and a rather uniform pattern for n-alkanes with concentrations falling below 41.4 microg/g. A significant contribution of an unresolved complex mixture indicated anthropogenic petroleum contamination. Further study of relevant indexes and geochemical biomarkers supported a mixed-source input of aliphatic hydrocarbons. With regard to PAHs, there was strong evidence that their dominant origin is pyrogenic. Finally, considerable excursion in delta(13)C(org) was attributed to changes in dissolved inorganic carbon accompanied by increased input of effluents and recycling of organic carbon within the lake, whereas the rise in isotopic composition of nitrogen was associated with agricultural runoff and sewage input from the town of Ioannina.