Reed straw 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, it can partially remove pollutants from terrestrial and aquatic ecosystems, offering clear environmental benefits. On the other hand, heavy metals can bind to functional groups in hemicellulose, lignin, and cell walls, thereby inhibiting sugar hydrolysis, anaerobic digestion, microbial fermentation, and enzymatic saccharification, resulting in lowering product yields and increasing operating and downstream processing costs. From a biorefinery perspective, this dual function presents both opportunities and challenges. This study investigates how heavy metals affect substrate structure and pretreatment performance, as well as their fate and removal during pretreatment of metal-contaminated reed biomass. Reed straw (Phragmites australis) contaminated with cadmium (Cd), lead (Pb), and zinc (Zn) was subjected to liquid hot water, alkali, and organosolv pretreatments to promote structural disruption and delignification. Furthermore, a mild acid prewashing step was introduced before the high-removal heavy-metal pretreatment to desorb metal ions associated with weakly bound functional groups in hemicellulose and lignin, without causing significant structural degradation of the lignocellulosic matrix. By reducing the initial heavy-metal load, the prewashing step minimizes metal-induced inhibition of pretreatment reactions and downstream processing and enabling a clearer assessment of heavy-metal 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). 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 contaminated lignocellulosic resources and offers significant insight into the behavior of heavy metals during biomass pretreatment. This study investigates how heavy metals affect substrate structure and pretreatment performance, as well as their fate and removal during pretreatment of metal-contaminated reed biomass. Reed straw (Phragmites australis) contaminated with cadmium (Cd), lead (Pb), and zinc (Zn) was subjected to liquid hot water, alkali, and organosolv pretreatments to promote structural disruption and delignification. Furthermore, a mild acid prewashing step was introduced before the high-removal heavy-metal pretreatment to desorb metal ions associated with weakly bound functional groups in hemicellulose and lignin, without causing significant structural degradation of the lignocellulosic matrix. By reducing the initial heavy-metal load, the prewashing step minimizes metal-induced inhibition of pretreatment reactions and downstream processing and enabling a clearer assessment of heavy-metal 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). 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 contaminated lignocellulosic resources and offers significant insight into the behavior of heavy metals during biomass pretreatment.