It has been frequently found that lacustrine branched glycerol dialkyl glycerol tetraethers (brGDGT)-derived temperatures are warm-season-biased relative to measured mean annual air temperature (AT) in the middle to high latitudes, the mechanism of which, however, is not very clear. Here, we investigated the brGDGTs from catchment soils, suspended particulate matter (SPM) and surface sediments in different water depths in Gonghai Lake in northern China to explore this question. Our results showed that the brGDGT distribution in sediments resembled that in the SPM but differed from the surrounding soils, suggesting a substantial aquatic origin of the brGDGTs in the lake. Moreover, the increase in brGDGT content and decrease in methylation index with water depth in sediments suggested more contribution of aquatic brGDGTs produced from deep or bottom waters. Therefore, established lake-specific calibrations were applied to estimate local mean annual AT. As usual, the estimates were significantly higher than the measured mean annual AT. However, they were similar to (and thus actually reflected) the mean annual lake water temperature (LWT). Interestingly, the mean annual LWT is close to the measured mean warm-season AT, thus suggesting that the apparent warm-season bias of lacustrine brGDGT-derived temperatures could be caused by the discrepancy between AT and LWT. In our study region, ice forms at the lake surface during winter, leading to isolation of the underlying lake water from air and hence higher LWT than AT, while LWT basically follows AT during warm seasons when ice disappears. Therefore, we think that lacustrine brGDGTs actually reflected the mean annual LWT, which is higher than the mean annual AT in our study location. Since the decoupling between LWT and AT in winter due to ice formation is a universal physical phenomenon in the middle to high latitudes, we propose this phenomenon could be also the reason for the widely observed warm-season bias of brGDGT-derived temperatures in other seasonally surface ice-forming lakes, especially in shallow lakes.