Passive sampling has recently been developed as an alternative to grab or average automated sampling, in order to obtain at lower cost, more realistic estimates of the average concentrations of organic contaminants in surface waters. The aim of this study was to develop and validate the in situ application of stir bar sorptive extraction (SBSE) as a passive sampling technique for the monitoring of 16 pesticides in a small river of an agricultural watershed located in the Beaujolais region. Stir bars (Twister®) were deployed for several periods of one or two weeks during two one-month campaigns in 2010 and in 2011. With prior in-lab calibration, the in situ application of SBSE allowed the integration of a quick concentration peak and the determination at lower cost of average concentrations of the target pesticides similar to those obtained from water samples collected by an automated sampler.