The generalization of ecological results from temporary streams needs the study of those ecosystems across a broad scale of running waters, covering the geographical ecological constraints involved (e.g., precipitation, temperature and geology). For the particular situation of Mediterranean streams in Southern Europe, high changes in water level, with unpredicting flood events, represent an important factor determining the structure and function of Mediterranean streams. This variability, inducing accentuated changes in the macroinvertebrate community, tends to influence the assessment methodologies. A set of metrics commonly used in Europe to assess organic degradation (Shannon-Wiener index, evenness, richness, BBI, IBE, BMWP , ASPT , DSFI, EPT, number of Trichoptera families, percentage of Gasteropoda, Oligochaeta and Diptera) and a multimetric index (IM9) developed to assess organic degradation in southern siliceous Portuguese basins were tested to evaluate quality at two contrasting sites (one unimpaired and another impaired by an identified point source of pollution). The multimetric index (IM9) composed by: ASPT (average score per taxon); GOLD (one minus percentage of Gasteropoda, Oligochaeta and Diptera); and TRICF (number of Trichoptera families), was the most suitable assessment methodology. IM9 presented a quite stable temporal pattern from February in late winter until June in early summer, even under the effect of episodic floods. A stepwise regression showed that most of tested metrics were significantly related to environmental variables (soluble reactive phosphorous, dissolved inorganic nitrogen and dissolved oxygen). Only richness, IBE and BMWP were not significantly influenced by environmental variables. Future research must be done covering the complete gradient of organic degradation, including the extension of multimetric assessment methodologies to temporary streams located in other regions under different geological and climatic conditions.