The toxic effects of waters collected from irrigation channels in a Mediterranean wetland (Albufera Natural Park, Valencia, Spain) were tested with the Microtox assay and compared with six pollution indices (PIs) defined from analytical parameters. Chemical oxygen demand (COD), biological oxygen demand (BOD), nutrients, heavy metals and pesticides were measured. The bioassay result (concentrations of the water sample (% V/V) that reduced light emission to 10%, 20% and 50%, EC10, EC20 and EC50, respectively (ECs)) was compared with the PIs. This comparison has demonstrated a general agreement between ECs and PIs, except in the case of irrigation channels affected by herbicides used in rice farming (molinate and thiobencarb). No pronounced inhibition was detected in the bioluminescence in relation to the eutrophic parameters in the irrigation waters for EC50 values, indicating that this parameter does not suffice to detect eutrophic waters. Data derived from irrigation water pollution and bioassay were assembled by multivariate statistical techniques (principal component analysis). These components were associated with various contamination sources.