The Gulf of Elat/Aqaba exhibits high inter-annual variability in mixed layer depth. Observations from the northern Gulf show differences of hundreds of meters in winter mixing depth, which ranges between 300 m in years with shallow mixing and up to 700 m in years with deep mixing. Deep mixing events can occur in two consecutive years or after four consecutive years of shallow mixing. The mixing depth has an effect on the concentration of nutrients and chlorophyll (and other tracers) in the surface and deep water. Using a 3D coupled physical-ecological model, we study the effect of shallow vs. deep mixing on the processes controlling the phytoplankton bloom and on nutrient accumulation in the deep water. We found that years with deep mixing are characterized by larger spatial variability in surface and integrated chlorophyll concentration during the mixing season. We also found that horizontal advection is more important for integrated phytoplankton concentration in years with deep mixing in the northern Gulf. Even when mixing was deep and nutrient limitation decreased, light limitation on growth was enhanced more in the north compared with the south. In addition, we showed that the nutrient accumulation in the deep water after a year with deep mixing of the northern Gulf was initially affected mostly by physical processes (such as advection and vertical mixing), and less from ecological regeneration and switched gradually to be dominated by ecological processes alone during the third year of shallow mixing.