This paper presents long-term data (1997–2008) on zooplankton obtained every 10 days in the open water of the Maloye More (Small Sea) Strait of Lake Baikal. Data on mean annual water temperature in Bolshye Koty Bay have been used for the 0-15 m layer. The dynamics of abundance of the major taxonomic groups (copepods, cladocerans and rotifers) is analyzed according to the conventionally distinguished years – “cold, warm and usual”. Changes in the structure and dynamics of some species (C. kolensis) and whole groups of organisms (rotifers and cladocerans) caused possible by water warming. The abundance of C. kolensis, D. galeata and B. longirostris is in positive correlation with water temperature.