Shellfish farming, a key sector of French aquaculture activity, allows the production of oyster spat in a controlled environment. Their production in commercial hatcheries requires control over the quality of the seawater used to sustain crossbreeding, breeding, and the production of fodder microalgae. Therefore, improving the filtration conditions of incoming water is crucial in ensuring the sustainability of production. An ultrafiltration pilot plant was therefore installed at Vendée Naissain. This ultrafiltration pilot plant allows filtration at 0.02 µm; it is used upstream of hatcheries to eliminate pathogens and parasites that can influence the development of cultivated species and downstream to remove oyster gametes in hatchery effluents. The objectives of this work were: (i) to use ultrafiltered seawater for the culture of the microalga Isochrysis lutea (T-Iso) to determine whether better growth than that observed with borehole water, historically used by the producer, can be achieved; and (ii) to determine whether the use of ultrafiltered water results in better fertilization rates of the cupped oyster Crassostrea gigas compared to filtered and UV-treated seawater. Ultrafiltered water has shown definite efficiency for culturing T-Iso with rapid growth and significant reduction in contamination compared to cultivation in well water. The contribution of ultrafiltered water in hatching is more nuanced; ultrafiltered water does not stabilize hatch rates, and its quality is highly dependent on the quality of the seawater used.