Agricultural farms are prone to pesticide contamination, with handling and disposal occurring before and after each spray. These activities, which result in point-source contamination, are the main cause of soil and water pollution (surface and groundwater). Farm contamination by pesticides is bioremediated through a system called a biobed. The study aims to evaluate the effects of physicochemical and biological factors on degradation efficiency and to optimise the system for improved performance. At least 50 % lignocellulosic substrate was required for effective degradation of the pesticide. Among coconut fibre, rice husk and coffee husk, coconut fibre exhibited greater pesticide degradation due to its higher carbon/nitrogen (C/N) ratio. Degradation of pesticides was increased with cotton fibre from 50 to 81.7 %. Novel biomixture’s containing amendments such as ash, biochar and digestate increased the biomixture's removal efficiency. Even complete sorption of fipronil was achieved at the lowest level of wheat biochar (1 %). Temperature varied 13–20 °C increased the degradation rate and 99 % 2,4-D degraded within 21 days. Optimal pesticide degradation was achieved at 60 % of the water-holding capacity. The dissipation rate of pesticides was higher under a 15-day pre-incubation period than under a 7-day period. Bioaugmentation with microorganisms including Anthracophyllum discolor, Streptomyces sp., Phanerochaete chrysosporium, Lentinula edodes and Trametes versicolor increased pesticide degradation. For example, A. discolor degraded atrazine 18 times faster than the control.