The datasets include measurements of water levels and water temperature profiles in Lake Kinneret, in summer, during the period (2000 – 2020). Lake Kinneret is located in Israel. Shipboard measurements of water temperature profiles were taken at the deepest point of ~40 m near the lake center (32.82 N; 35.60 E). The AML MINOS X probe was used (specifications are available online at https://geo-matching.com/ctd-systems/minos-x-ctd/svp). Data of water temperature profiles are associated with the Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research (http://kinneret.ocean.org.il/ar_3d_vb.aspx ). Data of Lake Kinneret water levels are associated with the Israel Water and Sewage Authority (https://www.gov.il/en/departments/water_authority/govil-landing-page ). Data format: xlsx file. There are two sheets in the Excel file: the first sheet includes water temperature profiles, while the second sheet includes lake water levels, in summer, during the period (2000 – 2020).