Vertical oxidation pond operated in sequencing batch mode (HRT: 1.25day) with duckweed as the vegetation was used to acclimatize with simulated agricultural wastewater. The maximum removal rate of urea [371g/(m3.d)] and COD [222.4g/(m3.d)] were observed at moderate concentrations of urea (500mg/L), N-P-K (60mg/L), and pesticide (20mg/L). Inhibition and toxicity posed by higher concentrations, decreased the removals of urea (83% to 61%), COD (81% to 51%), and TDS (76% to 50%) at the end of the acclimatization. Steady removal (> 99%) of PO43--P was observed during acclimatization. Effluent pH increased due to the generation of NH4+-N (maximum 370 ± 5mg/L) from the assimilation of urea. Oxidation of ammonia led to the maximum generation of NO2--N and NO3--N of 10mg/L and 9mg/L, respectively. Particles less than 300μm increased, and both specific gravity (from 2.62 to 2.42) and maximum dry density (from 1.73 to 1.30g/cm3) of the base soil decreased with an increase in urea, N-P-K, and pesticide. Reactor biomass increased (1.42 to 1.90g/L) up to initial concentrations of urea (500mg/L), N-P-K (60mg/L), and pesticide (20mg/L), then decreased (1.68g/L) with an increase in concentration.