a b s t r a c t The Water Framework Directive (WFD) strengthened the need for environmental quality assessment with rapid and accurate results. Studies of estuarine benthic macrofauna communities often use 0.5-mm mesh sieves in samples processing. However, this represents a considerable increase in sampling and identification effort compared to the use of 1-mm mesh sieves. Therefore, it is relevant to determine if mesh size matters in environmental quality assessments. The objectives of this study were as follows: (i) to test whether sieves with different mesh sizes provided different environmental status assessments in transitional systems, (ii) to compare the performance of different ecological indicators based on data from 0.5-and 1-mm mesh sieves and (iii) to compare the costs involved in using these two mesh sizes. Data were collected in the fall of 2007 and winter of 2008 at four sampling stations located in the Mon-dego Estuary, Portugal. The relative performance of Margalef and Shannon–Wiener indices, AMBI—AZTI Marine Biotic Index, Pielou, Eco-Exergy and Specific Eco-Exergy indices was analysed. Additionally, the multimetric Benthic Assessment Tool (BAT) was applied. The samples from the 1-mm mesh sieve were processed 2.9 times faster than the samples from the 0.5-mm mesh sieves. As expected, the density, biomass and number of species retained in the 0.5-mm mesh sieve were significantly higher in both seasons than the density, biomass and number of species retained in the 1-mm mesh sieve. All indicators were significantly different for the two mesh sizes in at least one season. The Pielou index was signifi-cantly different for the two mesh sizes in both seasons. Most indices showed that the 0.5-mm mesh sieve captured more information from the study system. The first BAT analysis provided different Ecological Quality Status (EQS) assessments for the two mesh sizes. To use the EQS obtained from the 1-mm mesh sieve as a proxy for the EQS for the 0.5-mm mesh sieve, further modifications were done in terms of reference conditions and class boundary thresholds. Regarding the Mondego Estuary, the use of a 1-mm mesh sieve appeared to be advantageous on routine environmental quality assessment, giving unbiased results with relatively less effort. Nevertheless, the methodology needs further validation and additional tests.