Vertical mixing affects the vertical transport of biochemical materials and modifies the characteristics of basin‐scale internal waves in subtropical, subalpine Yang Yuan Lake (YYL), in the north central region of Taiwan. Vertical mixing in YYL is generally caused by typhoons (strong winds and heavy rainfalls) during the spring, summer and early fall, or by cooling of the water column during late fall and winter. Vertical mixing caused by typhoons significantly affects internal thermal dynamics and biochemical processes, with basin‐scale internal waves enhanced before complete mixing occurs, and temporal variations of water temperature dramatically changing after typhoon events. This study quantitatively determines when the complete mixing (defined as homogenous temperature in a water column) occurs on the basis of the balance between kinetic energy and potential energy and also shows what meteorological conditions contribute to the vertical mixing. Data on water column thermal profiles and meteorological variables were collected by a wireless, instrumented buoy in the deepest location of YYL and from a nearby meteorological station, from spring 2004 to summer 2006. This study also investigated how a physical process (internal waves) is affected by the mixing associated with typhoons. Signal processing and a two‐layer model of the water column are used to understand the characteristics of basin‐scale internal waves.