There is increasing evidence that benthic cyanophytes in Mediterraneancalcareous streams can influence the macroinvertebrate community, probablydirectly due to toxicity. A study was therefore planned to establish whetherthis also influenced the results of indices used for the biological monitoringof stream water quality. Two indices (BMWPc based on macroinvertebrates; IBDbased on diatoms) widely used to assess water quality based on the diversity ofmacroinvertebrate and diatom assemblages were calculated for two unpollutedMediterranean calcareous streams in north-east Spain. The toxicity levelsof the cyanophyte communities were quantified by the Microtox test. There was aclear inverse relationship between the dominance of cyanophytes and the valuesobtained for the biological indices. It is recommended that cyanophyte biomassshould be incorporated in some way in the calibration of index values; the useof phycobiliprotein concentration and/or the chlorophyll a:phycobiliproteinratio is proposed.