Eutrophication and warming of lakes are occurring globally. Lake Baikal, a large ancient lake composed of three basins, has recently experienced benthic eutrophication at local sites and lake warming in the south basin. Here, we look for signals of warming and pelagic eutrophication across the entire lake using physical and biological data collected at a subset of 79 stations sampled ca. annually (1977–2003) during the period of summer stratification. Lake-wide, surface waters warmed 2.0°C; and, consistent with this warming, the abundance of two warm-water, cosmopolitan zooplankton taxa increased between two (pelagic cladocerans) and 12-fold (Cyclops kolensis). C. kolensis increased throughout the lake, whereas cladocerans increased significantly only in the north basin. In contrast, abundance of the cold-water endemic copepod, Epischura baikalensis, that dominates the crustacean zooplankton community, did not change. With the exception of one coastal station in the north basin, there is no evidence of pelagic eutrophication. Although chlorophyll concentrations increased 46% lake-wide (0.82 to 1.20μg/L), the increasing trend was significant only in the south basin. Surprisingly, mean Secchi transparency increased by 1.4m lake-wide across the 26-year time series with significant deepening of water transparency occurring in the central and north basins. This suggests a decline in productivity in the north and middle basins, but an increase in the south basin. Taken together, these findings suggest that physical and biological changes associated with warming have occurred in Lake Baikal, but wide-spread pelagic eutrophication in the lake's three basins has not.