Stable isotope (deuterium – ²H and oxygen-18 – ¹⁸O) surveys of water in Lake Ladoga and several rivers and small lakes within its watershed were conducted during 2012–2018. Over these 6 years, specific spatial and time differences in water isotope composition of Ladoga and small water bodies and streams were found. These differences depended firstly, on wetland type and the lakes distribution on the watershed and secondly, on groundwater discharge and type of lithological substrate (geological sediments or crystalline rocks). Besides landscape, climate (air temperature, precipitation, evapotranspiration) is a main physical factor which controls all scales of the stable isotope variations. In modern times, the sub-latitudinal gradient of climate but also presence of permafrost in the past effects the stable isotope variation. The isotopic composition divides the tributaries of Ladoga into three groups with a wide range of δ¹⁸O seasonal variations, and a significant atmospheric component. The isotopic composition of Ladoga water is generally stable ranging from δ¹⁸O = −11.7 to −9.5‰ (average δ¹⁸O = −10.6‰), δ²H = −84 to −74‰ (average δ²H = −78‰). The effect of evaporation is clearly seen due to accumulation of deuterium and oxygen-18 and a shift to the right from the Local Meteoric Water Line of δ²H versus δ¹⁸O diagram. In Lake Ladoga there is a local deviation of δ¹⁸O which can be explained by subaqueous discharge of groundwater from Riphean sediments.