Monitoring pesticides in the environment requires the use of sensitive analytical methods. However, existing methods are generally not suitable for analyzing small organisms, as they require large matrix masses. This study explores the development of a miniaturized extraction protocol for the monitoring of small organisms, based on only 30 mg of matrix. The miniaturized sample preparation was developed using fish and macroinvertebrate matrices. It allowed the characterization of 41 pesticides and transformation products (log P from −1.9 to 4.8) in small samples with LC-MS/MS, based on European guidelines (European Commission DG-SANTE, 2019). Quantification limits ranged from 3 to 460 ng g−1 dry weight (dw) for fish and from 0.1 to 356 ng g−1 dw for invertebrates, with most below 60 ng g−1 dw. Extraction rates ranged from 70% to 120% for 35 molecules in fish. Recoveries ranged from 70% to 120% for 37 molecules in macroinvertebrates. Inter-day precision was below 30% for 32 molecules at quantification limits. The method was successfully applied to 17 fish and 19 macroinvertebrates collected from two ponds of the French region of Dombes in November and May 2018, respectively. Both sample matrices were nearly always contaminated with benzamide, imidacloprid-desnitro, and prosulfocarb at respective concentrations of 42–237, 3, and 30–165 ng g−1 dw in fish, and 62–438, 2–6, and 15–29 ng g−1 dw in macroinvertebrates. Results show that this method is an effective tool for characterizing polar pesticides in small biotic samples.