Over the last 20 years, the Mondego estuary, Portugal has experienced excessive growth of macroalgae especially in the inner parts of the system, with several algal species implicated. In this study, we compare the effects of morphologically different species, the red alga Gracilaria verrucosa and the green macroalga Enteromorpha intestinalis on macrobenthic assemblages, by a field experiment whereby the biomass of algae was manipulated and the resultant changes in macrofauna abundance evaluated. The experiments were carried out in different areas (a relatively undisturbed sea grass bed and an upstream eutrophic area) experiencing different degrees of overall enrichment. Measurements of sediment redox potential revealed a rapid anoxia with a significant increase in algal biomass after 4 weeks. The effects of macroalgae were different at the two sites, being more marked in the eutrophic area. In addition, the effects of Gracilaria and Enteromorpha were significantly different, with Enteromorpha having a greater detrimental effect for most of the macrofauna, in particular Cyathura carinata, Scrobicularia plana, Cerastoderma edule and Alkmaria romijni. However, three of the most abundant invertebrates (Hydrobia ulvae, Hediste diversicolor and Capitella capitata) showed significant increases in abundance in weed affected compared to weed-free plots. Gracilaria had less of an impact on macrobenthic assemblages leading to a more enriched community. Between-site differences in overall impact were related to their previous disturbance history. (C) 2004 Elsevier B.V. All rights reserved.