Our study aimed at elucidating the role of internal loading in the budget of phosphorus (P) and assessed the importance of resuspension and diffusive fluxes for P cycling in large, shallow Lake Peipsi. The internal loading of P was quantified by a mass balance approach that considered the gross sedimentation of P as a component. The gross sedimentation of P was measured with sediment traps during May–October 2011. Additionally, we followed the monthly dynamics of diffusive fluxes and resuspension of P within this time period. The gross sedimentation of P dominated the mass balance calculations in Lake Peipsi. The resuspension of P constituted 62–68% of the gross sedimentation of P, and thereby accounted for the bulk of the total internal P load. Until late July, the release of P by diffusion was similar in magnitude to that of resuspension. Since August, resuspension was of governing importance for P cycling: the release of P by resuspension at that time was about 40-fold higher than that of the diffusion. Therefore, diffusion and resuspension provided a continuous supply of P to the water column during the growing season.