ABSTRACT. – The Water Framework Directive requires that the European Union countries determine the biological state of their waters with respect to sites of high quality. Although bioindicators have been widely applied in running waters and deep lakes throughout Europe, little is known about their applicability in shallow lakes and wetlands. The objective of this work is to check the effectiveness of epiphytic diatoms as indicators of the trophic state in two wetlands of Álava Province (N Spain). Diatom and water chemical samples were collected during summer and autumn 2007, following standard methodology. Stems of submerged macrophyte (Carex riparia, Iris pseudacorus, Veronica anagallis-aquatica) were sampled in each lake. Based on the number of statistically significant correlations between diatom indices and environmental factors, the SID index was show as the most suitable method to assess nutrients within these systems. SID was significantly correlated with TP, NTK and ammonium levels. Among three different plants, only the indices calculated from I. pseudacorus samples were significantly correlated with nutrients.