A growth model was developed to optimize the management of multi-trophic aquaculture systems by analyzing the influence of light and biomass stocking density (SD) in the productivity of Ulva ohnoi fed with the effluents from Solea senegalensis culture tanks. Growth rates and productivity were determined in three flat bottom algae tanks with different incident photon irradiances (E0) (163, 280, and 886 μmol photons m−2 s−1), photoperiod 12:12 h, and with stocking densities ranging from 82 to 340 gdw m−2. The distribution of photon irradiance in the algae tanks was estimated as a function of the E0 and SD. The results obtained showed that the algae exposed to the highest E0 (886 μmol photons m−2 s−1) and SD below 170 gdw m−2 showed a strong decrease in their growth rate, together with morphological changes. The model proposed to estimate the specific growth rate (μNET), on the basis of E0 and SD, assumed that photosynthetic activity is dependent on the local photon flux density and, therefore, spatially distributed in the tank. Non-linear regression used to estimate the growth kinetic parameters showed a standard deviation of the distance between measured and fitted μNET data values equal to 0.011 day−1. In terms of biomass productivity per unit area (BPA), the model shows, for each E0 level, a trend to increase with SD, achieving a maximum BPA, where SD can be considered optimal, and decreasing for higher SD values. The optimal SD and the maximum BPA achievable can be also determined as a function of E0.