Geologic remote sensing studies often targets surface cover that is supposed to be invariant or only changing on a geological timescale. In terms of surface material characteristics, this holds for rocks and minerals, but only to a lesser degree for soils (including alluvium, colluvium, regolith or weathered outcrop) and not for vegetation cover, for example. A view unobstructed by clouds, vegetation or fire scars is essential for a persistent observation of surface mineralogy. Sensors with a continuous multi-temporal operation (e.g., Landsat 8 OLI and Sentinel-2 MSI) can provide the data volume needed to come to an optimal seasonal acquisition and the application of data fusion approaches to create an unobstructed view. However, the acquisition environment always changes over time, driven by seasonal changes, illumination changes and the weather. Consequently, the creation of an unobstructed view does not necessarily lead to a repeatable measurement. In this paper, we evaluate the influence of weather and resulting soil moisture conditions over a 3-year period, with alternating dry and wet periods, on the variance of several “geological” spectral indices in a semi-arid area. Sentinel-2 MSI data are chosen to calculate band ratios for green vegetation, ferric and ferrous iron oxide mineralogy and hydroxyl bearing alteration (clay) mineralogy. The data were used “as provided”, meaning that the performance of the atmospheric correction and geometric accuracy is not changed. The results are shown as time-series for selected areas that include solid rock, beach sand, bare soil and natural vegetation surfaces. Results show that spectral index values vary not only between dry and wet periods, but also within dry periods longer than 45 days, as a result of changing soil moisture conditions long after a last rain event has passed. In terms of repeatability of measurements, an overall low soil-moisture level is more important for long-term stability of spectral index values than the occurrence of minor rain events. In terms of creating an unobstructed view, we found that thresholds for NDVI should not be higher than 0.1 when masking vegetation in geological remote sensing, which is lower than what usually is indicated in literature. In conclusion, multi-temporal data are not only important to study dynamic Earth processes, but also to improve mapping of surfaces that are seemingly invariant. As this work is based on a few selected pixels, the obtained results should be considered only indicative and not as a numerical truth. We conclude that multi-temporal data can be used to create an unobstructed view, but also to select the data that give the most repeatability of measurements. Images selection should not be based on a certain number of days without rain in the days preceding data acquisition but aim for the lowest soil moisture conditions. Consequently, weather data should be incorporated to come to an optimal selection of remote sensing imagery, and also when analyzing multi-temporal data.