This is the first study with the greatest number of multimetric indices calculated in Iran to assess water quality at Jajrood and Karaj protected rivers. Given the point that these rivers supply  a large portion of Tehran's drinking water, the present study aims at determining ecological quality of these rivers based on a suitable biotic index among these indices. Physicochemical and macro-invertebrate samples were collected with three replications during three consecutive years from 19 stations with a Surber sampler. In the Jajrood River, macroinvertebrates with 6667 abundance belong to 22 families and in the Karaj River, macro-invertebrates with 13,246 abundance belong to 24 families have been identified. The most appropriate time for sampling is in summer because of the existence maximum abundance and diversity of macroinvertebrates. The results of CCA have been shown physicochemical parameters TSS, EC, pH, and BOD have the most effect on the distribution of macroinvertebrates. Among the 16 biotic indices, the FBI index in Karaj River and the BMWP/ASPT index in the Jajrood River are the most reliable indices for assessing the water quality. The results showed that point pollution sources (orchards, restaurants and villages) and nonpoint sources (tourism activities and recreational area) have the most negative impact on the ecosystem of these two rivers. Results of water quality assessment have been shown the changes in ecological quality of water due to human activities; therefore, it is necessary to increase control and management of pollutant sources to improve the water quality of these two rivers.