Aim: Micro-scale processes play a fundamental role in shaping groundwater ecosystems and yet they remain poorly understood and under-explained. Here, we aim to provide an overview of existing concepts, methods, and knowledge. We outline how increased understanding of micro-scale processes may lead to an improved appreciation of the range of ecosystems functions taking place at different scales.

Main concepts covered: A reason why the groundwater ecosystems studies on the micro-scale are scarce lies in the fact that sampling is rarely carried out at the scale at which microorganisms and their grazers and predators, act. Within a larger scale framework in terms of geochemical features, supply with energy and nutrients, and exchange intensity and dynamics, the micro-scale adds heterogeneity which enables a wider range of redox reactions. Such processes are relied upon in bioremediation and we demonstrate that ecosystem modeling must consider the micro-scale.

Main methods covered: We describe the scales at which field sampling and laboratory investigations usually occur, and explain how such results should be interpreted. An appropriate tool for deriving knowledge on the micro-scale will be models which have to be carefully validated wherever possible. Examples of micro-scale models are provided, both experimental and computational, that so far only cover prokaryotes but can be developed further to incorporate more elements of the food web.

Conclusion/outlook: Models encompassing the micro-scale and whole food web processes, parameterized by experiments and investigations on the appropriate scale, may provide tools for testing concepts and improving our understanding of the subsurface ecosystems functioning.