Lake Victoria is a transboundary ecosystem shared by Kenya, Uganda, and Tanzania that supports capture fisheries, aquaculture, food security, transport, domestic water use, and biodiversity. Cage aquaculture is expanding in the basin, but its environmental effects vary with site conditions, hydrodynamics, stocking biomass, feed inputs, farm management, and background water quality. This policy-oriented opinion paper argues that commercial fish seed production and early nursery operations represent a distinct regulatory control point for biosecurity, genetic containment, traceability, and auditability. Although Kenya, Uganda, and Tanzania have regulatory frameworks addressing aquaculture, fish seed, environmental assessment, confinement, and hatchery operations, and regional LVFO/EAC instruments provide guidance on cage farming, fish seed certification, aquatic animal health, and natural nursery areas, an explicit and harmonized regional rule governing commercial hatchery and nursery activities in the open waters of Lake Victoria remains limited. The paper proposes a precautionary regional approach under which commercial artificial breeding, egg incubation, broodstock conditioning for seed production, fry nursing, and fry-to-fingerling multiplication are conducted outside the open waters of Lake Victoria. Narrowly defined and time-bound research or conservation activities could be considered following rigorous risk assessment. Controlled facilities equipped with screened water intakes and outlets, effluent and sludge management, appropriate biosecurity measures, health certification, genetic provenance records, traceability systems, and live-fish movement permits should provide seed to authorized grow-out operations. This approach could strengthen responsible aquaculture governance while supporting ecosystem protection, biosecurity, and sustainable fish production in the Lake Victoria basin.