The float bed tobacco seedling production system has been widely adopted in Zimbabwe due to increasing international pressure to phase out the use of ozone depleting methyl bromide. However, algae and root rot caused by Pythium spp. are a major challenge in this production system in Zimbabwe. These two problems are attributed to the constantly moist environment providing extended periods of leaf wetness and promoting succulent plant tissues, which favour the growth of algae as well as the development and spread of fungal diseases. Reports indicate that various oxidising agents and fungicides applied into the float water can be used to manage these two problems. Therefore, an experiment was set up to evaluate a Quaternary Ammonium Compound (QAC), an oxidizing agent [potassium permanganate (KMnO₄)], copper oxychloride and two systemic fungicides [metalaxyl and probamocarb-HCl] for the management of the two problems. The systemic fungicides were also tested in combination with QAC, KMnO4 and copper oxychloride. The QAC, KMnO4 and copper oxychloride were applied in the float water at sowing while the systemic fungicides were applied at 5 - 6 weeks after sowing as a float water treatment. The trial was first done in a greenhouse and repeated in the seedbed. In both trials, none of the treatments had an adverse effect on seedling germination and survival. At the early stages of seedling growth, before the systemic fungicides could be applied, algae were controlled best by QAC and copper oxychloride. Results also indicate that QAC in combination with metalaxyl provides the best (P<0.05) algae control throughout the seedling growth period, while metalaxyl on its own and in all three combinations gives excellent (p<0.05) control of Pythium root rot.