The ecotone concept is used to consider exchanges of matter and energy between groundwater and surface water systems. Ecotones control these exchanges by acting as a combination of three types of filter: the contrast between permanent darkness and day-night alternation produces a photic filter; the matrix of interstitial underground systems creates a mechanical filter which slow, down water velocity; biological and chemical processes, which often occur simultaneously, define a biochemical filter. The permeability of these filters changes according to water velocity. Thus, for ecotones between a surface system and a porous aquifer with large substrate pore size, dynamics of permeability are governed by hydrology, whereas between a surface system and a partially clogged aquifer with small substrate pore size, they are governed by aerobic and anaerobic processes. According to the degree of permeability, ecotones can be classified as either permanent or temporary sinks for the two adjacent systems. In the latter case, matter fluxes are retained in the ecotone, often undergoing transformation before being released to one of the ecosystems.