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Implementation of the European Union Water Framework Directive and associated national guidelines has emphasized the value of using biota, such as epilithic diatoms in streams, as indicators of water quality. However, guidelines for evaluating diatom samples have been established without explicitly evaluating their statistical robustness. We used epilithic diatom samples from 73 streams in northern Sweden and simulated the effects of variations in the counting sum size and taxonomic resolution of classifications for two indices indicating pollution (Indice de Polluo-sensibilité Spécifique, IPS) and acidity (acidity index for diatoms, ACID). Instead of the stipulated 400, we found that a count sum of 40 diatom valves for 50 streams, and 80 valves for 60 streams, would have been sufficient to obtain the same IPS index classification. The ACID index is more sensitive to count sum reductions, since the same classification would only have been obtained for 12 streams with 40 counted diatom valves or 24 streams with a count of 80 valves. Excluding rare taxa had negligible effects on the IPS and ACID indices. Excluding taxa occurring with less than 1.0% frequency affected the IPS classification of only one stream, and excluding taxa with less than 2.5% and 5.0% frequencies affected those of just one and no streams, respectively. The ACID index was affected for none, five, and 12 streams, respectively. At least in relatively unpolluted regions such as northern Sweden, our simulations suggest that a simplified methodological approach with site-specific counting sum sizes and reduced taxonomical resolution could be adopted, taking into account the way sites are classified in relation to established class boundaries. The simplified method is a step forward in improving the cost efficiency for stream monitoring, as costs of diatom analysis to obtain identical IPS and ACID classifications of our streams could be reduced considerably. Before the simplified method can be widely adopted, further simulations including regions with a higher proportion of polluted streams are required.