The role of mixoplanktonic algae is increasingly recognised as an important link between primary production and microbial loop processes, particularly in dystrophic systems where staining can both limit light and nutrient availability and increase bacterial productivity. We hypothesised that these three factors would affect the relative abundance of mixotrophs (RAmixotrophs), with increased light and nutrient availability decreasing RAmixotrophs and increased bacterial availability increasing RAmixotrophs. We employed a fully factorial design within near-shore mesocosms in a highly stained lake, with light intensity, bacterial abundance, and phosphorus concentration as treatment variables. Over the initial 3 days of the experiment, when changes were greatest, we found no significant three-way interaction effect among light, phosphorus and nutrients on the RAmixotrophs. We did find significant two-way interactions between phosphorus and light, and phosphorus and bacteria. RAmixotrophs was decreased by the addition of phosphorus whether light was added or not, but light only significantly deceased RAmixotrophs when phosphorus was not added. Phosphorus concentration was also found to decrease RAmixotrophs whether bacterial food was supplemented or not, but bacteria increased RAmixotrophs only in mesocosms without phosphorus additions. Collectively, our results indicated that phosphorus concentrations may be the primary driver of mixoplanktonic phytoplankton dynamics in dystrophic systems.