River–lake transition zones have been identified as major drivers of phytoplankton growth. With climate change reducing the frequency of complete lake overturns, it is expected that the Rhône River, the main tributary to Lake Geneva (France/Switzerland), will become the major source of nutrients for the lake euphotic zone. The river–lake transition zone was hence examined at the mouth of the Rhône River with the aim of understanding the complexities and controls of phytoplankton distribution in this specific deltaic ecosystem. Two field campaigns were carried out in which water samples were collected from longitudinal and transversal transects across the transition zone. These samples were analyzed for both nutrient and phytoplankton concentrations, while the fraction of Rhône River water in a lake sample was determined by the stable isotope composition of the water. The results indicate contributions in P and Si related to the Rhône intrusion into the lake. Furthermore, this river–lake transition zone appears to be a dynamic area that can locally present optimal conditions for phytoplankton growth. In early spring, a wind event broke the early and weak stratification of the lake, forcing the Rhône River and its turbidity plume to intrude deeper. Thus, this sharp drop of the turbidity within the euphotic zone allowed an increase in the phytoplankton biovolume of 44%. In early fall, outside of the turbid near field of the river mouth, the Rhône interflow, located just below the thermocline, promoted a local deep chlorophyll maximum.