Up to 95% of the contamination of surface water by pesticides comes from on-farm point sources in connection with washing and preparation operations. This contamination is a growing concern for environment and human health. Because of their efficiency, their low cost and their friendly and simple use, Biobeds were recognized as the best tool to treat these pesticide effluents. Assuming a single passage of the effluent through the Biobed followed by release of the percolate, the research focused on the efficiency of the depuration after a single percolation. Accounting for unknown hazards such as metabolites and bound residues leads, however, local rules in Europe to enjoin a recycling of the effluent until full evaporation to prevent any release in the environment. Managed as such, we show that the Biobeds are waterlogged and no longer perform the elimination of the effluent. This induces large hazards of either direct volatilization or effluent release, and goes with increased costs, dissatisfaction or demotivation of the farmers, thus jeopardizing the development of this solution. Accounting for these new depuration conditions leads to a new Biobed paradigm, namely optimization of the transpiration of the water rather than optimization of the single percolation depuration, which leads to sharp changes in Biobed forms, content and management. Moreover, the corresponding new system shows larger performance, decreased space and maintenance requirements, and improved aesthetics. This is shown in the present study based on compared monitoring of the systems performance, hydrodynamics and substrate conditions during use.