The effects of light and ammonium levels on net production, fluorescence parameters and non-structural carbohydrates of the seagrass Zostera noltii under different phosphate conditions were studied. A fully factorial design was used with light (low/high levels), ammonium supply and phosphate preculture conditions of the plants as the experimental variables. Both ammonium supply and low light caused negative and synergistic effects on net production, while ammonium toxicity was more severe at high light levels; in this case, it was independent of the non-structural carbohydrate (sucrose and starch) content. Preculturing of plant with added phosphate alleviated the ammonium toxicity, and also attenuated the negative production balance of plants grown at low light levels. The results indicated that phosphate preculture ameliorated the plant’s short-term response against the assayed stressors (low light, high ammonium) significantly. An overall consumption of non-structural carbohydrates in response to environmental stressors was recorded throughout the experiment, indicating the importance of carbon and phosphorus reserves to cope with adverse conditions. In addition, phosphate deficiency increased the vulnerability of plants, which could have negative ecological consequences for seagrass species thriving under phosphate deficiency conditions, or in developing seagrass transplantation programs.