Ecological indices tracking distinct impacts along disturbance-recovery gradients in a temperate NE Atlantic Estuary – Guidance on reference values Heliana Teixeira a, * , Fuensanta Salas b , Joa ˜o M. Neto a , Joana Patrı ´cio a , Rute Pinto a , Helena Verı ´ssimo a , Jose ´ A. Garcı ´a-Charton b , Concepcio ´ n Marcos b , Ange ´l Pe ´ rez-Ruzafa b , Joa ˜o C. Marques a a IMAR – Institute of Marine Research, University of Coimbra, 3004-517 Coimbra, Portugal b Department of Hydrology and Ecology, Faculty of Biology, University of Murcia, Spain article info Article history: Received 27 November 2007 Accepted 23 July 2008 Available online 31 July 2008 Keywords: estuary benthic invertebrates eutrophication physical disturbance ecological indicators reference values abstract Results gathered from a monitoring programme on the Mondego Estuary (Western Coast of Portugal) were compliant with findings drawn from other studies, which pointed out that unstable environments, namely estuarine systems, constitute a great challenge for the use of environmental tools such as ecological indices. The Margalef Index, the Shannon–Wiener Index and AMBI were proposed to evaluate the ecological status of benthic communities in the scope of the European Water Framework Directive (WFD) in Portugal and other European member states. In this system these indices were not equally effective in tracking changes in benthic communities that expressed obvious responses to anthropogenic disturbances (eutrophic situations and severe physical disturbance) and to subsequent impacts’ cessa- tion. Natural variability played an important role on the indices’ response, with estuarine gradient and habitat heterogeneity affecting the ranges of values obtained, and with extreme climate events slowing down the ongoing recovery process. Nonetheless, both natural and anthropogenic variability during the study period could be satisfactorily detected if we accounted for the information provided by all three indices. Based on the whole range of variation observed (a) as a response to different kinds of impacts, and (b) along recovery gradients, as well as accounting for the natural driving forces acting upon estuarine benthic invertebrate communities, we propose a set of reference values for these three indices. This proposal aims at contributing to the implementation of classification tools within the scope of the European WFD. Ó 2008 Elsevier Ltd. All rights reserved. 1. Introduction Ecological indicators are meant to illustrate the status of a system based on information from its components. The ecological condition of estuarine systems is rather difficult to assess due to natural stressors that could mask the response of potential ecological indicators. For instance, regarding benthic invertebrate based indicators, natural dominance of species in estuarine communities, as well as strong recruitment events, coupled with longitudinal and vertical gradients along estuaries lead to great variability of indices’ behaviour. This variability is not always associated with disturbance, in this way making it difficult to detect such an occurrence, if it was to be present (Mackey and Currie, 2001; Dauvin, 2007; Elliott and Quintino, 2007). The European Water Framework Directive (WFD, 2000/60/EC) establishes an outline for the protection of all waters (including inland surface waters, transitional waters, coastal waters, and groundwater), aiming at achieving a good quality status for all waters by 2015. The concept of ecological status developed in the WFD is defined in terms of the biological community quality, as well as the systems’ hydrological and chemical characteristics. Applying the WFD, it requires methods capable of distinguishing between different levels of ecological quality to classify surface waters (Borja et al., 2004; Borja, 2005). Experience demonstrates that none of the available measures of disturbance effects may be considered ideal. But the combination of different measures results as a good toolset for determining the ecological quality status (Bettencourt et al., 2004; Borja et al., 2004). In this sense, the results of the TICOR project (Typology and Refer- ence Conditions for Portuguese Transitional and Coastal Waters) (Bettencourt et al., 2004) include a method that combines a suite of indices. Recently, several approaches have been considering the possibility of combining different existent metrics into general indices of ecological quality: the M-AMBI in Spain (Borja et al., 2004; Muxika et al., 2007); the IQI in the United Kingdom and Republic of Ireland; the DKI in Denmark; the NQI in Norway and the BQI in * Corresponding author. E-mail address: helianateixeira@ci.uc.pt (H. Teixeira). Contents lists available at ScienceDirect Estuarine, Coastal and Shelf Science journal homepage: www.elsevier.com/locate/ecss 0272-7714/$ – see front matter Ó 2008 Elsevier Ltd. All rights reserved. doi:10.1016/j.ecss.2008.07.017 Estuarine, Coastal and Shelf Science 80 (2008) 130–140