A 1-year monitoring experiment of the Sarno River basin was conducted during 2008 to evaluate the overall quality of the water over time and to compare the results with those obtained previously. The physico-chemical and microbiological characteristics of the water course had not changed appreciably with respect to previous determinations, thus emphasizing the major contribution of untreated urban wastewater to the overall pollution of the river. Moreover, attention was paid to the perchlorate ion, one of the so-called emerging contaminants, which is widespread in natural environments and is known to have adverse effects on the human thyroid gland. Over the entire monitoring program, we did not find appreciable levels of perchlorate, although the particular environmental condition could support its development. Thus, a dedicated study was designed to assess the presence of bacteria that can reasonably reduce perchlorate levels. By enrichment and molecular procedures, we identified α- and β-Proteobacteria strains, classified by 16S rDNA sequences as Dechlorospirillum sp. and Dechlorosoma sp., respectively. Further physiologic characterization and the presence of the alpha subunit gene (pcrA) of the perchlorate reductase in both strains confirmed the presence in the river of viable and active perchlorate dissimilatory bacteria.