We investigated drifted and benthic macroinvertebrate in 2.5 to 17.6 ha headwater streams covered by Japanese cypress and cedar forest. This study was conducted K2, K3, and KR catchments located in FM Karasawayama in Tochigi prefecture. K2 catchment was subjected for 50% forest thinning from June to October in 2011, while K3 and KR catchments were represented as references. We collected 24hr-drifting samples for 8 times from March to December, 2011. Benthic samples were collected at pools and riffles of 50 m section of each stream for three times. For all macroinvertebrates, we identified taxa and classified their life types and functional feeding groups. Dry mass was estimated by either head width or weighted after drying. Chironomidae, Nemouridae, and Dixidae were dominated for all streams. Number of drifted invertebrates became higher during the months with heavy storm events. Significant difference did not occurred for the most of taxa and functional feeding groups among streams. Our findings revealed that effects of flooding on stream macroinvertabraes appeared to be greater than by ones at the first year of forest harvesting. Continuous monitoring for at least a few years for evaluating the confound impacts of forest harvesting and flood disturbances.