Streams and rivers are the most threatened and exploited freshwater ecosystems worldwide. Land-use changes, particularly the conversion of forests to agricultural, residential and industrial areas, have greatly impacted them, leading to declining water quality and biodiversity loss. Thus, evaluating rivers and identifying threats is crucial to protect and rehabilitate them adequately. A combination of physical, chemical and biological indicators in assessing the ecological conditions of aquatic ecosystems is now a prerequisite. Most river biomonitoring studies focus on benthic macroinvertebrates. However, river biomonitoring is not commonly practiced in the Philippines as it is not implemented regularly and officially. Nonetheless, several studies on the Philippine freshwater ecosystems have used benthic macroinvertebrates to assess the condition of streams and rivers. This mini-review describes the degree of taxonomic identification used in the Philippines to assess the ecological health of river systems. Moreover, it highlights the taxonomic quality assurance and quality control (QA/QC) system, or the lack thereof, to make bioassessment and biomonitoring more effective. Using Google Scholar, we conducted a quantitative search of studies that assessed water quality and condition of rivers using macroinvertebrates published from January 2000 to December 2021. Of the 945 search results, 31 studies satisfied the criteria for inclusion in this mini-review. These studies identified macroinvertebrates to order (3), family (13), genus (13) or species (2) level. Furthermore, taxonomic identification in over half of the studies (54.8%) was made by taxonomists (4), museum curators (5), and trained graduate students (8), while the remaining 14 studies (45.2%) had no information on taxonomic competency. Nonetheless, five of these 14 studies cited taxonomic reference guides. With 30 of 31 studies conducted by academic institutions and one government agency following, freshwater biomonitoring is still viewed as a purely academic endeavor.