This article reports the results of 3 field campaigns conducted in Lake Issyk-Kul in 2015, 2016, and 2017. Vertical CTD profiles were obtained and water samples collected at the total of 75 stations. Some biogeochemical and thermohaline parameters at the lake surface were also mapped at high horizontal resolution along the ship’s track. In addition, thermistor chains were deployed at 3 mooring stations in the eastern littoral region of the lake, yielding 147 days long records of temperature data. The measurements revealed that while the thermal state of the active layer, as well as some biogeochemical characteristics, were subject to significant interannual variability mediated by atmospheric forcing, the haline structure of the entire lake was remarkably stable at the interannual scale. Our data do not confirm the reports of progressive warming of the deep Issyk-Kul waters as suggested in some previous publications. However, they do indicate positive trend of salinity in the lake’s interior over the last 3 decades. A noteworthy newly found feature is a weak but persistent salinity maximum below the thermocline at the depth of 70–120 m, from where salinity slightly decreased downwards. The data from the moored thermistor chains support previously published hypothesis about significant role of the submerged ancient riverbeds on the eastern shelf in advecting littoral waters into the deep portion of the lake during differential cooling period. We hypothesize that the less saline littoral water penetrating into the deep layers due to this mechanism is responsible for the abovementioned features of salinity profile, and substantiate this hypothesis by estimates based on simple model assumptions.