The Upper Sakarya River System (USRS) is one of the most important river systems in Turkey. Its primary drainage is provided by the Porsuk Seydi and Bardakçı Rivers and their tributaries. Long term benthic invertebrate community structure in the USRS was investigated from 1995–2015 (with sampling conducted every five years) in order to assess changes in their composition and in relation to water quality. Oligochaete specimens sorted from samples were identified to the species level when possible; all other invertebrate specimens sorted from samples were identified to order and family level. In addition, some environmental parameters (e.g., dissolved oxygen, temperature, and hydrogen ion concentration as pH) were measured in situ. Although Ephemeroptera-Plecoptera-Trichoptera fauna were the most abundant group in fauna of USRS during the years 1995, 2000 and (in part) 2005 (18.80, 17.69, and 14.07%, respectively), this ratio decreased to 7.90% during the more recent years of monitoring. In 1995, 2000 and 2005, Nais bretscheri, Chaetogaster diastrophus, Chaetogaster langi, Pristinella jenkinae, Aulodrilus pigueti, Aulodrilus pluriseta, Potamothrix hammoniensis, and Psammoryctides albicola were the dominant oligochaete taxa. After 2005, tubificine species became more prevalent in samples. While 6 stations had high BMWP (Biological Monitoring Working Party) value in 1995, 2000 and 2005, only 1 station had high value after 2005. Values of Shannon Diversity Indices ranged from 2.00 to 3.05 for the years 1995–2000, 1.87 to 2.24 for the years 2000–2005, 1.06 to 1.85 for the years 2005–2010, and 0.97 to 1.80 for the years 2010–2015. In USRS, while values of dissolved oxygen were measured as 8.00 mg/l and 9.00 mg/l in 1995 and 2000, this high value was measured only at one station in 2015. It was found that numerical and proportional distributions of benthic invertebrates in the USRS have changed considerably between 1995 and 2015. It is obvious that these changes are the result of anthropogenic habitat degradation.