During the first two Strateole 2 campaigns, instruments were flown under super-pressure balloons at between 18 and 20 km altitude for several weeks at the Equator and performed in situ measurements of water vapour. This article describes the methodology used to quantify the modulation of water vapour by atmospheric waves and deep convective cases. This methodology allows us to bring to light the influence of atmospheric waves and extreme deep convection on the observed water vapour anomalies.