Ulva are green algae known for their biomass accumulation on the coast due to eutrophication. As these algae are able to bioremediate nitrate loadings, they are used as biofilters of enriched waters in aquaculture. Ulva form a holobiont by naturally hosting various microbes, also involved in nitrate metabolism. However, little is known about fluctuations of the Ulva holobiont in fertilized waters over time. We surveyed fluctuations of the bacterial community associated with Ulva lacinulata cultivation, with (enriched, ENR) and without (seawater only, SW) nitrate-based fertilization. Ulva biofilm and cultivation water were regularly collected and contextual parameters (nutrients, temperature, pH) were regularly measured over twelve weeks. Metabarcoding of the 16S rDNA in the biofilm and water compartments revealed that fertilization led to higher alpha-diversity. Diversity patterns indicated that samples clustered together for each compartment in SW or ENR. Fertilization led to a different genus composition in the water after 5 days, and it led to a more even community in the biofilm, from few very dominant genera at the beginning of the experiment to more less dominant genera at the end. The core microbiota in the biofilm common to SW and ENR was mainly composed of genera involved in the host fitness and physiology. Core genera common to SW and ENR in the water were likely beneficiating from the culture conditions. Microbiota's predicted metabolic pathways revealed a heightened capacity for nitrate reduction in ENR. These results may serve as a foundation to understand nitrate loadings impact on Ulva's microbiota in eutrophication conditions.