The spatial distribution of vegetative agricultural residuals (VAR) implies that any waste treatment system (WTS) designed to manage VAR is particularly sensitive to transportation costs. Additionally, a wide range of treatment technologies is potentially available for VAR treatment, but some of them lack a well-developed market for their output products. This study develops a method to design an economically feasible VAR treatment system, analyzing the profitability of the system as a function of logistics and uncertain market prices of the available treatment technologies' products. The design method includes an economic optimization model followed by a sensitivity analysis of the potential changes in the system’s profitability. The results show that the market price of the treatment technologies' products has a larger impact on the system’s profitability than transportation costs. Specifically, if biochar prices reach the level forecasted by experts, pyrolysis will become the dominant technology of the WTS. The research highlights the importance of the treatment technology selection and the location of treatment facilities in the design of an optimal WTS for VAR.