Diatoms of the family Epithemiaceae possess a unicellular nitrogen-fixing cyanobacterial endosymbiont. We investigated the potential of extracellular nitrogen and phosphorus concentrations to affect the endosymbiont load of Rhopalodia gibba O. Mull. and Epithemia turgida Ehr. in field and culture populations. In a growth chamber experiment, monoclonal cultures of R. gibba were exposed to three levels of nitrate-nitrogen. Nutrient-diffusing substrates were used in a lake environment to create nine microhabitats of varying nitrogen and phosphorus ratios for natural populations of R. gibba and E. turgida. The number of endosymbionts per diatom increased as ambient nitrogen became limiting; mean endosymbiont volume increased as nitrogen increased. The mean endosymbiont surface area: volume ration decreased with increasing nitrogen. Total endosymbiont volume per diatom (the product of the number of endosymbionts per diatom and their individual biovolumes) did not have a simple response to increasing nitrogen. Phosphorus limitation uncoupled the relationship between endosymbiont load and nitrogen. We suspect that flexibility of the endosymbiont load can reduce the metabolic cost to the diatom if the endosymbionts are dependent on the diatom for a resource.