Microtopography can have a large effect on flow processes at the soil surface and the composition of soil water. Microtopography is often represented by a roughness parameter in hydrological models. In areas without a strong topographical gradient, microtopography may be underestimated when accumulated in a single parameter, especially in shallow groundwater systems. This study reviews the intricate relationships between microtopography, surface runoff, and ecohydrology in systems featuring shallow water tables. We specifically focus on relations between microtopography and runoff, impact of microtopography on response times of shallow groundwater ecosystems, and microtopography and spatial distribution of groundwater quality parameters and site factors. We advocate the use of microtopography in modeling approaches by examples that feature typical ecosystems with shallow groundwater under influence of microtopography. With a simple modeling approach, we show how microtopography could add flexibility to the acrotelm–catotelm concept in raised bog hydrology. The classic acrotelm–catotelm concept hinders progress in understanding small scale hydrological variations and other ecohydrological relations. Furthermore, we illustrate possible self-organization properties of wetlands. Finally, we show how microtopography and surface runoff affect the mixing of water with different chemical signatures, resulting in variations of the occurrence of plant species.