The stratification in the Northern Gulf of Eilat/Aqaba follows a well-known annual cycle of well-mixed conditions in winter, surface warming in spring and summer, maximum vertical temperature gradient in late summer, and erosion of stratification in fall. The strength and structure of the stratification influences the diverse coral reef ecosystem and also affects the strength of the semi-diurnal tidal currents. Long-term (13 months) moored thermistor data, combined with high temporal and vertical resolution density profiles in deep water, show that transitions from summer to fall and winter to spring/summer occur in unpredictable, pulses and are not slow and gradual, as previously deduced from monthly hydrographic measurements and numerical simulations forced by monthly climatologies. The cooling and deepening of the surface layer in fall is marked by a transition to large amplitude, semi-diurnal isotherm displacements in the stratified intermediate layer. Stratification is rebuilt in spring and summer by intermittent pulses of warm, buoyant water that can increase the upper 100–150 m by 2 °C that force surface waters down 100–150 m over a matter of days. The stratification also varies in response to short-lived eddies and diurnal motions during winter. Thus, the variability in the stratification exhibits strong depth and seasonal dependence and occurs over range of timescales: from tidal to seasonal. We show that monthly or weekly single-cast hydrographic data under-samples the variability of the stratification in the Gulf and we estimate the error associated with single-cast assessments of the stratification.