To better understand the interaction between wind waves and the biological properties of freshwater ecosystems, it is highly desirable to reproduce coherent water motions generated by wind. This paper presents new 15 m3 mesocosms with wavemakers, also known as wave flumes, which are designed to emulate the effects of surface waves on the biological processes in shallow lakes. First, we succinctly review existing approaches to modify mixing of the water column in ecological studies: most mixing devices that have been used to date generate turbulence, but do not create the coherent water motions generated by surface waves. This justifies the development of mesocosms that seek to reproduce these coherent water motions. Tanks with wave generators are common devices in fluid mechanics, and we adapted them for aquatic ecology. Second, we describe the effects of waves on the water column, provide some theoretical background on wavemakers, and detail the choices adopted for the design of our device. Our system is able to generate waves with a wavelength of 0.1–5 m and amplitude of 1–5 cm in a 10 m long tank with a 1 m water column, which allows to choose mixing intensity from superficial to complete mixing of the water column. Experimental results show effects of mixing regime on water chemistry and plankton abundance. We finally discuss challenging research questions on the ecological role of surface waves in shallow lakes that can be addressed with mesocosms with wavemakers.