Animals affect ecosystems through consumption–excretion of food. Amphidromous shrimps frequently dominate low-mid altitude streams, where downstream connectivity to oceans is sustained. Although their direct influence on benthic communities has been studied, little is known about their influences on nutrient cycling. Here, we hypothesized that the dominance of shrimps alters nutrient mineralization by benthic macroinvertebrates in streams due to the difference in the quality and quantity of excretion between shrimps and aquatic insects. In the field manipulative experiment, the presence of shrimps slightly decreased the biomass of aquatic insects but tripled total benthic macroinvertebrate biomass directly through their own biomass. The mass-specific NH₄⁺ excretion rate by shrimps was similar to aquatic insects, and the areal NH₄⁺ excretion by benthic macroinvertebrates was increased by 2.5 times in the presence of shrimps. In contrast, shrimps excreted significantly less soluble reactive phosphorus (SRP) than aquatic insects, and the presence of shrimps did not affect areal SRP excretion by benthic macroinvertebrates. The field survey showed a positive correlation of NO₃⁻ concentration with the shrimp density, inferring that excess NH₄⁺ was immediately nitrified in the benthic zone, and NO₃⁻ was released into the water column. Although the nutrient concentration of stream water is frequently attributed to the condition of the watershed area, the results of this study indicate that downstream connectivity to oceans can also influence nutrient dynamics of the stream through the density of amphidromous shrimps.