Point source contamination of natural water resources by pesticides constitutes a serious problem and on-farm biopurification systems (BPS) were introduced to resolve it. This paper reviews the processes and parameters controlling BPS depuration efficiency and reports on recent biotechnological advances which have been used for enhancing BPS performance. Biomixture composition and water management are the two factors which either individually or through their interactions control the depuration performance of BPS. Which process (biodegradation or adsorption) will dominate pesticides dissipation in BPS depends on biomixture composition and the physicochemical properties of the pesticides. Biotechnological interventions such as augmentation with pesticide-degrading microbes or pesticide-primed matrices have resulted in enhanced biodegradation performance of BPS. Despite all these advancement in BPS research, there are still several issues which should be resolved to facilitate their full implementation. Safe handling and disposal of the spent biomixture is a key practical issue which needs further research. The use of BPS for the depuration of wastewaters from post-farm activities such as postharvest treatment of fruits should be a priority research issue considering the lack of alternative treatment systems. However, the key point hampering optimization of BPS is the lack of fundamental knowledge on BPS microbiology. The use of advanced molecular and biochemical methods in BPS would shed light into this issue in the future.