Certified organic flue-cured tobacco (Nicotiana tabacum L.) production has experienced significant expansion in the United States. Despite this expansion, there is very little information available that outlines organic nitrogen (N) programs for seedling production. To develop grower recommendations, research was conducted to evaluate the effects of a Peruvian seabird guano (SG), sodium nitrate (SN), or a combination of the two (SN_SG) in a float system on float water chemistry and seedling vigor. A conventional treatment (Conv; SQM Ultrasol Premium) was included for comparison. A greenhouse study was conducted twice between June 2016 and January 2017. Nitrogen fertilizer treatments were applied to tobacco float system water twice during the germination and growth of tobacco transplants. Float system water was collected every 5 days and analyzed for N forms, pH, dissolved oxygen, and bicarbonate. At the end of each experiment, transplant dimensions were measured and percent of usable plants collected. Float water bicarbonate concentration was <1 meq L−1 in treatments absent of SG for the duration of the study, but were in excess of 12 meq L−1 25 days after seeding (DAS) when SG was the exclusive N source. Despite high ammonium and bicarbonate concentrations with SG, neither factor negatively impacted seedling growth. Both SG and SN_SG produced as many usable plants as Conv; however, seedling height and diameter tended to be lower in SG compared to the other two treatments. No usable transplants were produced when SN was the sole fertility source, likely because of lack of nutrients other than N. Furthermore, many of the organic fertility products require biological activity to mineralize organic N to a plant-available form. This activity can have potentially detrimental outcomes on float system solution pH, dissolved oxygen, and bicarbonate levels.