New regulations on water quality require a close control of the possible biological activities known or unexpected pollutants may bring about. We present here a protocol based on the direct exposure of zebrafish to river water and the analysis of expression of specific genes in their scales to determine the presence of compounds with dioxin-like biological activity. The method does not require the killing of animals and allows detection of the biological activity after a single day of exposure. When tested, the method with real samples from the Llobregat River, clear temporal and spatial variations were observed, demonstrating its suitability for monitoring natural variations in water quality linked to specific discharges. High biological activities were unrelated to the currently checked water quality parameters (macropollutants, turbidity, TOC, etc.), but they did correlate with the presence of micropollutants (estrogens, detergents, etc.) related to domestic and/or industrial runoffs. The scale assay therefore provides a new tool to evaluate water quality changes that cannot be easily derived from the existing standard analytical procedures. It ranks among the very few described protocols able to detect biological effects from natural water samples, without a pre-concentration step, and after only 24 h of exposure.