While numerous detection methods exist for environmental heavy metal monitoring, easy-to-use technologies combining rapidity with in vivo measurements are lacking. Multiwell systems exploiting transgenic tadpoles are ideal but require time-consuming placement of individuals in wells. We developed a real-time flow-through system, based on Fountain Flow cytometry, which measures in situ contaminant-induced fluorescence in transgenic amphibian larvae immersed in water samples. The system maintains the advantages of transgenic amphibians, but requires minimal human intervention. Portable and self-contained, it allows on-site measurements. Optimization exploited a transgenic Xenopus laevis bearing a chimeric gene with metal responsive elements fused to eGFP. The transgene was selectively induced by 1 microM Zn(2+). Using this tadpole we show the continuous flow method to be as rapid and sensitive as image analysis. Flow-through readings thus accelerate the overall process of data acquisition and render fluorescent monitoring of tadpoles suitable for on-site tracking of heavy metal pollution.