The objective of this study was to determine the vertical distribution of metals and organic carbon in lakes Kucukcekmece and Terkos, which are located in different areas near Istanbul and are affected by different environmental factors. The aim was also to specify the metal input, its sources, and the ecological risk over the last 700 years. For analysis, core sediment samples were taken from the bottom of each lake, sliced into 2-cm sections, and analyzed for multiple elements, organic carbon, carbonate, and chlorophyll degradation products. It was determined that Lake Kucukcekmece is threatened by domestic and industrial pollution. To solve this problem, a treatment plant was commissioned in 2012 for the treatment of urban and industrial wastes. In addition, natural gas has been the preferred fuel for the last two decades in Istanbul and this has changed the pollutant profile. On the other hand, Lake Terkos faces possible risks of Mn, P, and As inputs because of fertilizer use in nearby agricultural fields.