AbstractLong‐term monitoring of ecosystem succession provides baseline data for conservation and management, as well as for understanding the dynamics of underlying biogeochemical processes. We examined the effects of deforestation and subsequent afforestation of a riparian forest of Japanese cedar (Cryptomeria japonica) on stable isotope ratios of carbon (δ13C) and nitrogen (δ15N) and natural abundances of radiocarbon (Δ14C) in stream biota in the Mt. Gomadan Experimental Forest and the Wakayama Forest Research Station, Kyoto University, central Japan. Macroinvertebrates, periphytic algae attached to rock surfaces (periphyton), and leaf litter of terrestrial plants were collected from six headwater streams with similar climate, topography, and bedrock geology, except for the stand ages of riparian forests (from 3 to 49 yr old in five stands and >90 yr old in one reference stand). Light intensity and δ13C values of both periphyton and macroinvertebrates decreased synchronously with forest age in winter. A Bayesian mixing model indicates that periphyton contributions to the stream food webs are maximized in 23‐yr‐old forests. Except for grazers, most macroinvertebrates showed Δ14C values similar to those of terrestrial leaf litter, reflecting the influence of modern atmospheric CO2 Δ14C values. On the other hand, the Δ14C values of both periphyton and grazers (i.e., aquatic primary consumers) were significantly lower than that of modern atmospheric CO2, and were lowest in 23‐yr ‐old forest stands. Previous studies show that root biomass of C. japonica peaks at 15–30 yr after planting. These evidences suggest that soil CO2 released by root respiration and dispersed by groundwater weathers carbonate substrata, and that dissolved inorganic carbon (DIC) with low Δ14C is incorporated into stream periphyton and some macroinvertebrates. The ecological response in the studied streams to clear‐cutting and replanting of Japanese cedar is much slower (~20 yr) than the chemical response (<5 yr). More than 50 yr is required for the food web structure to completely recover from clear‐cutting. The ecological delay is attributed to several biogeochemical factors, the understanding of which is critical to integrated management of forest–stream continuum and the prediction of ecosystem resilience in response to environmental change.