This study investigated the occurrence and seasonal distribution of different classes of pesticides in surface waters of the Ondas River Watershed, as well as potential risks to the aquatic health and human water consumption in the western region of Bahia state, Brazil. Two gas chromatography-mass spectrometry analytical methods were applied to monitor 34 pesticides in water samples collected during both the dry and rainy seasons at 17 sites. Upon individual analysis, only γ-HCH, methoxychlor, demeton-S, methyl parathion, fenitrothion, chlorpyrifos, and azoxystrobin exhibited statistically significant differences between seasons. During rainy season, concentration medians of residues were higher for γ-HCH (74.7 ng L−1), methoxychlor (25.1 ng L−1), and azoxystrobin (47.2 ng L−1), potentially linked to historical contamination or illegal use. Conversely, pesticides like methyl parathion, fenitrothion, and chlorpyrifos, belonging to the organophosphate class, showed higher concentration medians in the dry period, measuring 75.1, 5.50, and 10.8 ng L−1, respectively, probably due to region crop activities. The risk quotient (RQ) assessment for aquatic life indicated that 59.0% of the samples in the dry season and 76.0% in the rainy season had RQ values greater than one, signifying a critical scenario for species conservation. Regarding human consumption, elevated risks were observed for heptachlor in both sampling periods and for azoxystrobin during the rainy season, surpassing RQ levels above 1, indicating danger in untreated water ingestion. Additionally, 24.0% and 53.0% of the samples in the dry and rainy seasons, respectively, contained at least one pesticide exceeding the EU resolution limit (100 ng L−1). Therefore, considering this information, implementing mitigation measures to avoid the river's contamination becomes imperative.