Abstract: The Minjiang River, a first-order tributary of the Yangtze River, is located in the upper reach of the Yangtze River and flows through a basin with well-developed agriculture. To investigate pesticide pollution characteristics in the Minjiang River, surface water samples were collected from 25 representative locations in the upper and middle reaches. Liquid-liquid extraction followed by gas chromatography-mass spectrometry was employed to study the occurrence of 40 pesticides in the river for the first time. The results indicated that 18 pesticides from 5 classes were detected in the upper and middle reaches of the Minjiang River, including 5 pyrethroids, 7 organophosphates, 4 organochlorines, 1 triazole, and 1 dinitroaniline. Ten out of the 18 pesticides had detection frequencies of 100% with concentrations ranging from 0.66 to 459.77 ng/L. Pyrethroids were the primary pesticides detected, comprising up to 74.4% of the total concentrations. While most pesticides were detected in both the upper and middle reaches, their concentrations varied significantly. Principal component analysis revealed a clear distinction between the sampling points in the upper and middle reaches, with notable differences in the distribution characteristics of pesticides such as bifenthrin, fenpropathrin, triazophos, and diazinon between these areas. Correlation analysis showed significant positive correlations among pyrethroids (i.e., permethrin, bifenthrin, fenpropathrin, cyfluthrin, cyhalothrin), as well as between pyrethroids and chlorothalonil, phosalone, and triadimefon. Both pyrethroids and organophosphates exhibited a decreasing trend along certain river sections, indicating partial removal of pesticides in the Minjiang River. However, some sampling locations showed elevated pesticide concentrations. This study highlights the widespread presence of pesticides in the Minjiang River, with pyrethroids being the dominant contaminants, and reveals distinct characteristics of pesticide pollution in the upper and middle reaches. Moreover, it underscores the need to address non-point source pollution of pesticides in the Minjiang River Basin.