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[Display omitted] • The benthic community in the Sava River was predominantly colonized by pennate diatoms. • In the benthic community in the Tisa River centric diatoms were predominant. • rbcL marker provided a comprehensive view of the diatom community. • Presence/absence of taxa assessed with rbcL to assess water quality of large lowland rivers proved more similar to morphological identification. This study examines the effectiveness of digital microscopic and molecular analysis (rbcL and 18S markers) in assessing diatom community composition and water quality in two international rivers (Sava and Tisa rivers). Also, two different approaches were applied for calculating diatom indices: based on the relative abundance of taxa and the presence/absence of taxa. The rbcL marker showed up as a more suitable choice for providing a comprehensive view of the diatom community compared to 18S, which can be partly attributed to variations in the coverage of reference databases. Furthermore, both morphological and molecular analysis pointed out statistically different ecological statuses of investigated rivers. Diatom indices derived from molecular data indicated one or two classes of lower ecological status than those based on morphological analysis. However, the average diatom indices derived from molecular presence/absence data were higher than those based on the relative abundance of taxa. After summarizing all the results, we can recommend using the rbcL marker with taxa presence/absence data for routine monitoring of large lowland rivers. [ABSTRACT FROM AUTHOR]

• Small fish farms affected the ecological parameters and diversity of diatoms. • Chemical parameters in total explained the highest portion of variability. • Water quality, based on the majority of diatom indices, was assessed as good. • It is suggested to use the proposed TID RS for running waters in Serbia. • Review of Serbian legislation regarding the ecological status is necessary. The main aim of this study was to investigate the application of benthic diatoms and the efficiency of diatom indices in water ecological assessment of rivers in Serbia, as well as the influence of trout farms on rivers water quality. Research was conducted in one year period along the Crnica and Radovanska rivers (Eastern Serbia), in 11 sampling sites (taking into account the position of trout fish farms that are built on both rivers). Results showed that fish farms affect the physical and chemical parameters, as well as diversity of the epilithic diatom assemblage along the rivers. Canonical correspondence analysis (CCA) indicated that among tested physical and chemical parameters, conductivity "EC", water hardness "WH", sulfates "SO 4 2-", ionized ammonia fraction "NH 4 +", nitrates "NO 3 –", "pH", mud, stone and depth were the most important variables affecting the distribution of diatom species. A total of 206 epilithic diatom taxa were recorded in the Radovanska and 170 in the Crnica River. Based on diatom indices, trout fish farms have no significant negative impact on the water quality of the investigated rivers (indices are not enough sensitive). Redundancy analysis (RDA) showed a high degree of correlation between the majority of indices which mostly indicated to good water quality of studied rivers. TID and TDI were the only two indices indicating moderate and poor water quality of both rivers. Water quality based on the TID RS , the first proposed diatom index for Serbia was differ in two classes in most sites compairing with TID. [ABSTRACT FROM AUTHOR]