The contribution of terrestrially-derived carbon to micro-crustacean zooplankton biomass (i.e. allochthony) has been previously studied in lakes and reservoirs, but little is known about allochthony in rivers. We hypothesized that restricted selective grazing in turbulent environments such as rivers would decouple zooplankton from specific microbial and algal food resources, such that their allochthony would mirror the allochthonous contribution to the bulk particle pool. Allochthony was analyzed in 13 widely distributed Swedish rivers, using a dual-isotope mixing model. Zooplankton biomasses were generally low, and allochthony in different micro-crustacean groups (Cladocera, Cyclopoida, Calanoida) varied from 2% to 77%. As predicted, there were no correlations between allochthony and variables such as Chlorophyll-a or bacterial production. Instead, allochthony was similar to the terrestrial contribution in the particulate organic matter, with relationships close to 1:1. The total zooplankton community allochthony was strongly related to the ecosystem metabolic balance between production and respiration, which in turn was dependent upon the ratio between total autochthonous organic carbon concentrations and water color. Our study suggests that micro-crustacean allochthony is regulated differently in rivers compared to in lacustrine systems.