Brazil is among the ten largest rice producers in the world, concentrating its production in the southern region. Anthropic activities, such as the disposal of chemicals in the ecosystem and consequently in the aquatic environment, end up harming the availability and quality of the water. Here, we developed an analytical method based on BAµE with WAX as an extraction phase for the determination of 5 pesticides and 2 emerging contaminants in water samples used in rice cultivation by HPLC-DAD. The method was fully optimized through univariate and multivariate approaches. The optimized condition was obtained with 145 min of extraction time, without salt addition and 35 min of desorption time using 250 μL of MeOH:AcEt (60:40, v/v). A reduced mass of extraction phase (around 4 mg) and sample and solvent volumes (15 mL and 300 µL, respectively) were used. The bars have a low cost and can be used up to 20 times without loss of extraction efficiency. Furthermore, the developed method presented high-throughput, because it uses a Voltage Regulator Variac system that allows the coupling of six magnetic stirrers simultaneously. The LODs ranged from 1.67 to 2.50 µg L −1 and the LOQs ranged from 5.00 to 7.50 µg L −1 ; both were below the VMP established by Ordinance 2.914/2011/MS for drinking water. Relative recoveries applied to the sample ranged from 80 to 121%. The intra-day and inter-day precision were up to 14% and 19%, respectively. The results were satisfactory, in accordance with the validation guidelines of the AOAC. Twenty-four samples collected in the Camboriú River Basin, which is influenced by rhiziculture, were analyzed and the analytes were not detected, as they are below the limits obtained in this method.