The longitudinal functional connectivity of a river-lake-marsh system (RLMS) refers to the actual water-mediated transport of material from upstream to downstream areas along a spatial gradient and is fundamental to understand hydrological and biogeochemical cycles. However, due to a lack of consensus on appropriate data and methods, the quantification of connectivity is still a challenge, especially at the catchment scale. We developed a new method to evaluate longitudinal functional connectivity based on fluxes of materials (water, sediment, and chemicals) along a RLMS.