Yahuarcocha Lake (Ecuador) faces critical contamination from agricultural pesticide runoff, threatening ecosystem health and water security. This study assessed physicochemical water quality, pesticide concentrations, bacterial community structure, and toxicological effects of fenamiphos and 1,3-dichloropropene on microalgae bioindicators at thirteen sampling points during 2023. HPLC analysis revealed maximum fenamiphos concentration of 64.38 ppb (643-fold above WHO guidelines) and 1,3-dichloropropene of 9.67 ppm near agricultural zones. Physicochemical analysis showed severe organic pollution with COD reaching 10,314 mg/L and BOD₅ of 459 mg/L, exceeding TULSMA standards. DGGE molecular analysis demonstrated reduced bacterial diversity at contaminated sites, with Shannon-Wiener index declining from 1.792 to 1.099, indicating pollution-induced community shifts. Toxicity bioassays on Chlorella sp. and Desmodesmus sp. demonstrated 44-66% mortality, with fenamiphos (64% at 5 ppb) and 1,3-dichloropropene (66% at 10 ppb) confirming high toxicity through acetylcholinesterase inhibition. Cluster analysis revealed 100% bacterial community similarity among eight heavily polluted points, indicating severe selection pressure for pesticide-tolerant taxa. These findings provide evidence for implementing integrated watershed management including constructed wetlands, riparian buffers, and integrated pest management to protect this critically threatened Andean freshwater ecosystem.