A nitrogen manipulation experiment was conducted in a semi-intensive outdoor system where turbot larvae feed on copepods. Nitrogen addition is hypothesized to stimulate a cascade reaction increasing phytoplankton biomass, copepods’ productivity and larval fish survival. Triplicates were established for three treatments: a control with no additional nitrogen, a pulsed dose where nitrogen was added in three doses over time and a full dose where all nitrogen, equal to the total of the pulse dose treatment, was added initially. In the control, chlorophyll a averaged 3.3 ± 1.5 μg L−1 and phytoplankton was dominated by diatoms, while the pulsed and full dose treatments showed chlorophyll a at 28.6 ± 9.9 and 47.7 ± 10.0 μg L−1, respectively, with dinoflagellates as the main phytoplankton group. Due to photosynthesis, pH increased >9 in both the nitrogen treatments compared to the control (8.5). Potential toxic dinoflagellates, including Alexandrium pseudogonyaulax and Prorocentrum spp., became dominant in the nitrogen treatments and might have arrested zooplankton recruitment. Laboratory experiments with a toxic strain of A. pseudogonyaulax proved that Acartia tonsa reproduction and naupliar survival were affected negatively at realistic fish tank concentrations of 100 and 20 cells mL−1, respectively. Compared to the control, pulsed and full dose treatments reached higher copepod biomass and showed a shift over time in species composition from Centropages hamatus to Acartia spp. However, high pH levels and dinoflagellate blooms had a negative effect on larval fish survival, suggesting management improvements on water quality and separation between copepods and fish production tanks.