Sum-frequency generation (SFG) spectroscopy is frequently used to investigate the structure of monolayer films of long-chain fatty acids at the air-water interface. Although labeled a non-invasive technique, introducing intense SFG lasers onto liquid interfaces has the potential to perturb them. In the present work, narrowband picosecond SFG is used to study the structural changes that occur in palmitic acid and per-deuterated palmitic acid monolayers at the air-water interface in response to the high field strengths inherent to SFG spectroscopy. In order to determine structural changes and identify measurement artifacts, the changes in specific resonance intensities were measured in real-time and over a broad range of surface concentrations from films spread onto a stationary Langmuir trough. Using narrowband instead of broadband SFG minimizes the overlap of the incident infrared beam in the lipid C-H stretching region with resonances from the water sub-phase. Nevertheless, narrowband SFG still generates a thermal gradient at the surface, which produces a significant decrease in local concentration in the area of the laser spot caused by Bérnard-Marangoni convection originating in the sub-phase. The decrease in concentration results in an increase in the conformational disorder and a decrease in the tilt angle of lipid tails. Crucially, it is shown that, even at the highest monolayer concentrations, this gives rise to a measurement effect, which manifests itself as a dependence on the spectral acquisition time. This effect should be taken into account when interpreting the structure of monolayer films on liquid surfaces deduced from their SFG spectra.