Aquatic macroinvertebrates are affected by physical, chemical and biological conditions of the stream. Some of them are pollution-sensitive while others are pollution-tolerant. They are good indicators of stream health. This study was conducted to determine the status of Labo and Clarin Rivers using macroinvertebrates as bioindicators. Dip-net and kick-net methods were employed. Results showed that sampling sites in forested areas in Labo and Clarin rivers had a higher macroinvertebrate taxa richness and abundance. Mayflies (Ephemeroptera) were the dominant macroinvertebrates. Ephemeroptera, Plecoptera, and Trichoptera (EPT) and %EPT indices were higher in Clarin than Labo River. Based on Family-level biotic index (FBI), the water quality of sampling site 1 in Clarin (forested site) was excellent (organic pollution is unlikely) and very good (possible slight organic pollution) for site 1 in the Labo River but decreased downstream (fair to good quality). MANOVA results revealed a significant difference in the macroinvertebrate abundance in the agricultural sites of Labo River and forest sites of Clarin River. Cluster analysis showed that among the macroinvertebrates, mayflies (Ephemeroptera) were distinct in the forest sites and bugs (Hemiptera) in agricultural sites on Clarin River. Fly larvae (Diptera) and beetles (Coleoptera) were distinct in agroforest sites of the Clarin River while abundant in agricultural sites on Labo River. Results indicate a need for monitoring and proper management of Labo andClarin rivers to prevent increasing deterioration of water quality.