Some passive houses are provided a warm supply flow inlet coming from a mechanical ventilation system, creating issues of shortcut ventilation as a result of an originated density layer stratification, since the supplied warm air is confined to the ceiling level. In this way, there exist several complaints of thermal discomfort and poor indoor environmental quality in passive houses. Thus, a method of periodic variation of the ventilation supply frequency is an option to increase mixing, aimed at de-stratifying the room conditions. A small-scale water model is employed in order to systematically explore the influence of the created standing waves from the supply input frequency and its interaction with stratification characteristics in the studied volume, hence operating with water as a working fluid and a paddle as an oscillating mechanical input. Measurements at three different input frequencies and at three input paddle locations have been performed, gathering vertical temperature gradients and visualization data from them. Thus, ventilation efficiency of passive houses is set to improve, consequently increasing their public acceptability, via reaching buoyancy resonance, i.e., matching the input frequency with the internal Brunt-Väisäla frequency of the fluid. Consequently, the shortcut ventilation issues may be mitigated and the public acceptability of passive houses increased, achieving a higher thermal comfort and economic and energy demand savings, while enhancing sustainable and renewable heating alternatives such as the heat recovery from the outgoing exhaust flow.