Information is presented about the first stage of research within the Most important Innovative project of National Importance “RITM Carbon” to quantify carbon stocks and fluxes in aquatic ecosystems in a type 1 intensive testing site in the Kivach Nature Reserve (Karelia). The research is carried out as part of a program for monitoring carbon stocks and greenhouse gas (GHG) flows in aquatic ecosystems (water bodies, watercourses) of the boreal zone of North European Russia. Model water bodies were selected (Lake Chudesnaya Lamba, River Sandalka, Chechkin Stream) and a network of observation sites was formed. The landscape structure of the drainage area was studied, the hydrogeological conditions were characterized, and the groundwater table depths and chemical composition were determined. The chemical composition of water in the lake, river and stream in different seasons (mineralization, gas composition, pH, organic matter and nutrients) and the forms of carbon were determined. The lithology and chemical composition of bottom sediments were studied. Quantitative indicators of phyto-, bacterio- and zooplankton development were estimated. A weather station was installed on the shore of the lake and automatic stations were installed in the water column to measure the hydrophysical parameters (water temperature, solar radiation fluxes, currents) necessary to assess the gas transfer coefficient and GHG emissions. Original designs of stationary trapping chambers for monitoring gas emissions from bottom sediments were developed. The first experimental data on GHG fluxes from bottom sediments into the water and at the water-air interface were obtained.