Freshwater diatoms in the genera Epithemia and Rhopalodia, host obligate N2-fixing endosymbionts of cyanobacterial origin which are models for studying the evolution of organelles. Endosymbionts living in Epithemia cells are derived from a free-living cyanobacterial ancestor in the Cyanothece lineage. These endosymbionts now live inside host Epithemia cells, functioning as N-supplying organelles. Their numbers inside Epithemia cells increase with non-N nutrient additions (e.g., P), but decline as available N increases, in response to shifting stoichiometry and N economy of the Epithemia assemblage. Lacking both photosystems 1 and 2, the endosybionts cannot live on its own. We used NanoSIMS to analyze spatial and temporal patterns of C and N movement the between the diatom host and the endosymbiont. Results show that a significant amount of carbon fixed by the diatom host is transferred to the endosymbiont. Similarly, much of the nitrogen in the host cell was fixed by the endosymbiont. This is the first demonstration of carbon and nitrogen exchange between the endosymbiont and its diatom host. These measurements of intracellular biogeochemical fluxes provide insight into the mechanisms by which symbionts can evolve into organelles. Epithemia species are abundant in many freshwater ecosystems where nitrogen is limiting. Epithemia can live on inert substrates (rocks, sand) and can be a dominant epiphytic diatom living on the macroscopic green alga, Cladophora. We studied nitrogen and carbon fluxes of Epithemia living in the epiphyte assemblage to determine if N fixed in the diatom is transferred throughout the periphyton matrix. We found that nitrogen fixed by the symbiont is found in non-nitrogen fixing diatoms and also in Cladophora although at very low concentrations. We discuss how nitrogen fixation in diatoms versus in free living cyanobacteria can have major consequences for river food webs.