Abstract The internal cycles of carbon, silica, nitrogen, and phosphorus in the South and North Basins of Lake Baikal were quantified in the frame of a multidisciplinary collaboration. Fluxes of particulate organic matter from the epilimnion to the deep water were quantified with integrating sediment traps deployed at 200- to 250-m water depth and compared with fluxes measured in near-bottom traps to reveal mineralization in the water column. Sedimentation rates were determined with dated sediment cores to calculate mass accumulation rates of elements in the sediment. Advective and turbulent transport of dissolved nutrients in the water column was based on a set of monitoring data, which included temperature and current data, as well as hydrochemical data of the water column. Diffusive fluxes from the sediment to the overlying water column were determined by applying different porewater sampling techniques. The combination of these data resulted in consistent internal budgets for carbon, nitrogen, and phosphorus in Lake Baikal: the new production in the South Basin was 1730 mmol C m −2 year −1 and the mass accumulation rate in the sediment 220 mmol C m −2 year −1, whereas in the more secluded North Basin, new production was only 1220 mmol C m −2 year −1 and mass accumulation rate 125 mmol C m −2 year −1. Fluxes of particle-bound nitrogen, phosphorus, and biogenic silica were by about 30% smaller in the North Basin than in the South Basin. Export fluxes of nitrogen from the surface zone to the deep water were 150 mmol N and 100 mmol N m −2 year −1. Denitrification rates in the sediment were estimated from mass-loss calculation to 38 and 53 mmol N m −2 year −1 for the South and North Basin, respectively, corresponding to 25% and 52% of the total nitrogen input to the hypolimnion. Nitrogen (19 and 13 mmol m −2 year −1) was finally buried in the sediments of the South and North Basins; 10.1 and 3.5 mmol P m −2 year −1, and 1830 and 1400 mmol Si m −2 year −1 were transferred to the deep water in the South and North Basin where 28% and 70% P, and 64% and 54% Si were retained in the sediments. A diatom bloom occurred during our sampling period of 2 years, which usually occurs only every 3 to 5 years. Accordingly, Si flux data from sediment traps were increased by an estimated 50% compared with the long-term average illustrating the necessity of several years of field measurements to compensate for the natural dynamics of Lake Baikal.