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Lake Como receives inflows of vastly varying scales. The majority of the lake's water comes from the alpine inflows to the north, and much smaller inflows supply large amounts of pollutants in the south. We combined various data sets with a three‐dimensional hydrodynamic model to investigate the processes affecting the fate of these inflows with potential applications for management responses to both pollution and climate change effects. During the stratified period inflow waters from the northern alpine sources intrude in the metalimnion, undergo a deflection due to the Earth's rotation, and subsequently affect local flushing in a semi‐closed embayment receiving the shallower intrusions of the small polluted inflows.