Sampling at four salmon aquaculture sites along the west coast of Scotland has identified short-lived aggregations of planktonic hydrozoans (>280 individuals m−3), here termed blooms. Several such blooms were linked with increases in gill pathology and mortality in caged fish. Two types, Obelia sp. and Lizzia blondina, were found to cause blooms regularly and often concurrently. Species composition of hydrozoan populations and fluctuations in population sizes were spatially and temporally heterogeneous, with adjacent sites (within 30 km of one another and with similar oceanic exposure) experiencing no correlation between species composition and population density. Blooms appeared temperature-mediated, with all identified blooms by Obelia sp. and L. blondina taking place in water above 12 °C; however, temperature alone was not found to be predictive. Blooms were not significantly associated with change in salinity, water clarity, or photoperiod. Due to the apparent lack of broadly applicable predictors, we suggest that localized, targeted sampling and examination of planktonic hydrozoan populations is required to discern the presence or absence of a bloom. It is likely that many blooms have historically caused harm in salmon aquaculture while remaining unrecognized as the root cause.