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A combination of field observations and 3‐D hydrodynamic simulations were used to identify the phytoplankton species and to estimate the various time scales of the dominant physical and biological processes in Lake Iseo, a deep subalpine lake located in northern Italy, during a stratified period (July 2010). By ordering the rate processes time scales, we derive a phytoplankton patch categorization and growth interpretation that provides a general framework for the spatial distribution of phytoplankton concentration in Lake Iseo and illuminates the characteristics of their ecological niches. The results show that the diurnal surface layer was well mixed, received strong diurnal radiation, had low phosphorus concentrations and the phytoplankton biomass was sustained by the green alga Sphaerocystis schroeterii. The vertical mixing time scales were much shorter than horizontal mixing time scales causing a depth …