The largest freshwater ecosystem on earth is in the subsurface: the groundwater. It is populated by animals of almost all phyla and by bacteria, archaea, and fungi. Processes on the macro-, meso-, and micro-scale shape this ecosystem. Bioremediation, i.e., the degradation of contaminants, is steered on the scale of micrometers. However, processes that take place on the micrometer scale are still poorly understood and have not been studied extensively. They are usually lacking from models. In this communication, the plea for studying and making models for the processes that take place on the micrometer scale is based on the conceptual model of bottom-up effects of the pore scale environment. Such conceptual models may influence how quantitative models are built by structuring them.