AbstractSince the 1980s, the occurrence of harmful algae blooms (HABs) in the Persian/Arabian Gulf has increased concurrently with the rapid expansion of Gulf seawater desalination. Moreover, Gulf HABs have been observed simultaneously with established HABs in the adjacent outer ocean basin. The freshwater sink generated by seawater desalination is balanced by a stronger near-surface influx of the Gulf exchange flow, which carries salt into the Gulf and may also carry HABs that travel passively. Here, the hypothesis that seawater desalination has strengthened Gulf exchange influx, probably leading to accelerated horizontal advection of established HABs in the outer ocean basin into the Gulf and enhanced HAB dispersal within the Gulf, is examined. Two scenarios with differing magnitudes of freshwater loss from seawater desalination and one scenario devoid of freshwater loss are simulated in a coupled Gulf-Atmosphere Model and compared. The results show that, because of this freshwater loss, mean March–June exchange influx (outflux) strengthened by 3.93% (5.38%) and mean July–February exchange influx (outflux) weakened by −10.16% (−9.08%); flushing time decreased by ≈21 days, and peak exchange influx occurred sooner by ≈1 month. These results support the above-stated hypothesis and suggest a linkage between Gulf seawater desalination and the recent shift in the seasonal regime of Gulf HABs. This causal mechanism for the increase in Gulf HABs highlights the need for a basin-scale management strategy to monitor and forecast the Gulf’s state under the stresses of seawater desalination and provide early warning signs of environmental problems. Such a strategy is already in place in several marginal seas with anthropogenic activities. The findings here provide design elements for developing this strategy in the Gulf.