Multiple studies have been carried out on the correct estimation of the damages (direct tangible losses) associated with floods. However, the complex analysis and the multitude of variables conditioning the damage estimation, as well as the uncertainty in their estimation, make it difficult, even today, to reach one single, complete solution to this problem. In no case has the influence that the topographic relationship between the main floor of a residential building and the surrounding land have in the estimation of flood economic damage been analysed. To carry out this analysis, up to a total of 28 magnitude–damage functions (with different characteristics and application scales) were selected on which the effect of over-elevation and under-elevation of the main floor of the houses was simulated (at intervals of 20 cm, between −0.6 and +1 metre). According to each of the two trends, an overestimation or underestimation of flood damage was observed. This pattern was conditioned by the specific characteristics of each magnitude–damage function, meaning that the percentage of damage became asymptotic from a certain flow depth value. In a real scenario, the consideration of this variable (as opposed to its non-consideration) causes an average variation in the damage estimation around 30%. Based on these results, the analysed variable can be considered as (1) another main source of uncertainty in the correct estimation of flood damage, and (2) an essential variable to take into account in a flood damage analysis for the correct estimation of loss.