Fishponds are man-made shallow water bodies that are still little studied because of their small size. They represent high value ecosystems, both environmentally (biodiversity hotspot) and economically (fish production). They can have a high place on the hydrographic network, so their influence on water quality is of first importance for rivers and water bodies located downstream and monitored under the Water Framework Directive. These small water bodies can be a source of contaminants during draining period or an efficient buffer for pesticides. We wanted to evaluate whether these ponds could also be a remediation tool against metals by following the annual evolution of upstream/downstream flows. Cadmium, copper, lead and zinc concentrations were quantified in the dissolved phase upstream and downstream of three ponds, each one having a specific agricultural environment (traditional or organic). Metal concentration was quantified in sediments and water. For the dissolved phase, the predictive non-effect concentration was often exceeded, suggesting an environmental risk. Results highlighted also greater quantity of metals at the downstream of the pond compared to the upstream, suggesting remobilization into the ponds or direct cross-sectional contributions from the watershed (e.g. runoff from crops) or even remobilization. Regarding sediments, minimal contamination was shown but a high mineralogical variability. No buffer effect of ponds, which could reduce the risk of acute or chronic toxicity, was detected.