Reed straw (Phragmites australis) is an attractive and underutilized substrate for biorefinery applications due to its fast growth, low economic value, and reduced fire risk. When reed straw grows along contaminated water and soil, heavy metals can bind to functional groups in hemicellulose, lignin, and cell walls, thereby inhibiting sugar hydrolysis, enzymatic saccharification [1], microbial fermentation, and anaerobic digestion, resulting in lower product yields [2] and increasing operating and downstream processing costs [3]. This can lower the quality of reed biomass, but can also offer clear environmental benefits by using reed to reduce pollution levels in terrestrial and aquatic ecosystems [4, 5]. This study investigates how heavy metals affect substrate structure and pretreatment performance and sugar hydrolysis, as well as their fate and removal during pretreatment of metal-contaminated reed biomass. To understand how heavy metals can affect the process, contaminated Reed straw with cadmium (Cd), lead (Pb), and zinc (Zn), and an uncontaminated Reed were subjected to alkali pretreatment to promote structural disruption and delignification. Furthermore, a mild acid prewashing step was introduced before the main pretreatment of contaminated Reed straw to desorb metal ions associated with weakly bound functional groups in hemicellulose and lignin, without causing significant structural degradation of the lignocellulosic matrix. According to some literature [1, 6], reducing the initial heavy-metal load, the prewashing step minimizes metal-induced inhibition of pretreatment reactions and downstream processing, enabling a clearer assessment of metal ions behavior during the main pretreatment stages. Following pretreatment, both the solid and liquid fractions were hydrolyzed to determine lignin, hemicellulose, and cellulose using methods developed by the National Renewable Energy Laboratory (NREL) [7] and understanding the effect of heavy metals in this step, compared with the uncontaminated one. Atomic absorption spectroscopy (AAS) was employed to quantify heavy metal concentrations in untreated and treated samples. Overall, this study supports the development of sustainable process pathways for the utilization of contaminated lignocellulosic resources and offers significant insight into the behavior of heavy metals during biomass pretreatment.