Rising atmospheric temperature and CO2 impact all freshwater systems. In groundwater, one such impact is CO2- and temperature-induced weathering, which leads to more intense weathering of silicate rocks. Here, we tested whether the increased CO2 levels, the weathering, or rather the increasing temperature, impacted on fauna and prokaryotes in the groundwater ecosystem. We also conducted the analyses separately for two groups of wells, one of which contained wells that were secluded from the surface (and often rather deep), and wells tapping the quaternary aquifers (often rather shallow) which exchange with the surface more intensely. Organism abundances and relative composition did not correlate with temperature or CO2 levels. While many organisms rely on silica, in contrast, we found negative correlations between silica concentrations and fauna. The increases in silica concentrations over time, i.e. temporal trends, also partly correlated negatively with organisms. We hypothesize that the unexpected negative correlations are not direct effects, but indirectly indicate that groundwater communities do not adapt rapidly enough to changes in silica concentrations, but also more generally to changes for which silica might only be a proxy. Groundwater fauna take part in the ecosystem service of water self-cleaning and are thus considered beneficial for sustainable raw water for drinking water production. The propensity of groundwater fauna to decrease with increases in silica, jeopardizes future drinking water production.