Unicellular nitrogen fixing cyanobacteria (UCYN) are abundant members of phytoplankton communities in a wide range of marine environments, including those with rapidly changing nitrogen (N) concentrations. We hypothesized that differences in N availability (N₂ vs. combined N) would cause UCYN to shift strategies of intracellular N and C allocation. We used transmission electron microscopy and nanoscale secondary ion massspectrometry imaging to track assimilation and intracellular allocation of¹³C-labeled CO₂ and ¹⁵N-labeled N₂ or NO₃ at different periods across a diel cycle in Cyanothece sp. ATCC 51142. We present new ideas on interpreting these imaging data, including the influences of pre-incubation cellular C and N contents and turnover rates of inclusion bodies. Within cultures growing diazotrophically, distinct subpopulations were detected that fixed N₂ at night or in the morning. Additional significant within-population heterogeneity was likely caused by differences in the relative amounts of N assimilated into cyanophycin from sources externaland internal to the cells. Whether growing on N₂ or NO ₃, cells prioritized cyanophycin synthesis when N assimilation rates were highest. N assimilation in cells growing on NO₃ switched from cyanophycin synthesis to protein synthesis, suggesting that once a cyanophycin quota is met, it is bypassed in favor of protein synthesis. Growth on NO₃ also revealed that at night, there is a very low level of CO₂ assimilation into polysaccharides simultaneous with their catabolism for protein synthesis. This studyrevealed multiple, detailed mechanisms underlying C and N management in Cyanothece that facilitate its success in dynamic aquatic environments.