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This article addresses the problem of controlling the growth of microalgae originating in Mexican rivers, especially in the state of Sinaloa, Culiacan River. For this purpose, a robust, high-gain nonlinear observer is proposed to estimate the unknown disturbance in the cultivation of mixotrophic microalgae with the presence of organic nutrients. Once a perturbation function related to the change of ambient light is estimated, an output feedback control for the photobioreactor is proposed, in which through Lyapunov’s convergence functions, the final boundary stability conditions are obtained. Thus, a turbidity sensor was designed for Spirulina platensis, a native microalgae of Culiacan River, which is presented using the MATLAB-Arduino programming environment. This sensor is calibrated using biomass culture and is a low-cost device. Through the numerical study, the feasibility and performance of the control and the observer are evaluated. Finally, real-time experimental evaluations are made based on the literature, studying the use of robust controllers in a photobioreactor with a mixed culture, in the presence of environmental changes in lighting.