Carbaryl (a carbamate insecticide) and cypermethrin (a synthetic pyrethroid insecticide) are extensively used in agriculture. However, the presence of these insecticides in the environment constitutes a significant source of ecological contamination. This study determined the levels of these insecticides in Lisungwi, Neno District, a cotton-growing area in Southern Malawi. A total of 81 soil samples (500 g each) were collected from six sampling points (33 in dry season and 48 rainy season). A total of 86 water samples (500 ml each) were collected seasonally (20 from shallow wells, 18 from streams, and 48 from boreholes). High performance liquid chromatography (HPLC) was used to determine carbaryl while UV/Vis spectrophotometer detected cypermethrin. Paired t test showed a significant (p < 0.05) difference between rainy season carbaryl (in water and soil) and maximum recommended levels (MRL) (Canadian guidelines and Australian Guidelines). Similarly, a significant (p < 0.05) difference between carbaryl and WHO limits and US MRL was reported in water and soil during the rainy season. A similar observation was made for cypermethrin. Specifically, carbaryl (0.083–0.254 mg/ L in surface water and 0.165–0.492 mg/L in groundwater) and cypermethrin (8.115–15.460 mg/L in surface water and 4.48–12.18 mg/L in groundwater) concentrations during the rainy season were above the recommended limits. On the other hand, cypermethrin (0.01– 0.048 mg/L) in the soil samples during the rainy season was below the recommended limits while carbaryl (1.67–1.305 mg/L) was above the recommended limits. Higher carbaryl and cypermethrin values were recorded during the rainy season than the dry season. Nitrate, pH, and EC and the insecticides (carbaryl and cypermethrin) depicted strong correlation and significance (p < 0.05), suggesting that these factors influenced their persistence in both soil and water. The study provides evidence that Lisungwi has cypermethrin and carbaryl concentrations above the recommended limits and their presence varies with seasons—a situation considered to be a serious threat to both aquatic biota and humans.