Multi-proxy analyses of new piston core M13-08 together with seismic data from the Gulf of Gemlik provide a detailed record of paleoceanographic and paleoclimatic changes with special emphasis on the timing of the connections between the Sea of Marmara (SoM) and the Gulf of Gemlik during the late Pleistocene to Holocene. The deposition of a subaqueous delta sourced from the Armutlu River to the north is attributed to the lowstand lake level at -60 m in the gulf prior to 13.5 cal ka BP. On the basis of the seismic data, it is argued that the higher lake level (-60 m) in the gulf compared to the SoM level (-85 m) attests to its disconnection from the SoM during the late glacial period. Ponto-Caspian assemblages in the lacustrine sedimentary unit covering the time period between 13.5 and 12 cal ka BP represent a relict that was introduced into the gulf by a Black Sea outflow during the marine isotope stage 3 interstadial. Contrary to the findings of previous studies, the data suggest that such an outflow into the Gulf of Gemlik during the late glacial period could have occurred only if the SoM lake level (-85 m) was shallower than the sill depth (-55 m) of the gulf in the west. A robust age model of the core indicates the connection of the gulf with the marine SoM at 12 cal ka BP, consistent with the sill depth (-55 m) of the gulf on the global sea level curve. Strong evidence of a marine incursion into the gulf is well documented by the mu-XRF Sr/Ca data. The available profiles of elemental ratios in core M13-08, together with the age-depth model, imply that a warm and wet climate prevailed in the gulf during the early Holocene (12-10.1 cal ka BP), whereas the longest drought occurred during the middle Holocene (8.2-5.4 cal ka BP). The base of the main Holocene sapropel in the gulf is dated at 10.1 cal ka BP, i.e., 500 years younger than its equivalent in the SoM. The late Holocene is earmarked by warm and wet climate periods (5.0-4.2 and 4.2-2.7 cal ka BP) with some brief cold/dry periods (4.2 and 2.7-0.9 cal ka BP).