Increasingly, pathogen‐resistant (PR) plants are being developed to reduce the agricultural impacts of disease. However PR plants also have the potential to result in increased invasiveness of nontarget host populations and so pose a potential threat to nontarget ecosystems. In this paper we use a new framework to investigate geographical variation in the potential risk associated with unintended release of genetically modified alfalfa mosaic virus (AMV)‐resistant Trifolium repens (white clover) into nontarget host populations containing AMV, clover yellow vein virus (ClYVV), and white clover mosaic virus (WClMV) in southeastern Australia. Surveys of 213 sites in 37 habitat types over a 300 000‐km² study region showed that T. repens is a significant weed of many high‐conservation‐value habitats in southeastern Australia and that AMV, ClYVV, and WClMV occur in 15–97% of nontarget host populations. However, T. repens abundance varied with site disturbance, habitat conservation value, and proximity to cropping, and all viral pathogens had distinct geographic distributions and infection patterns. Virus species frequently co‐infected host plants and displayed nonindependent distributions within host populations, although co‐infection patterns varied across the study region. Our results clearly illustrate the complexity of conducting environmental risk assessments that involve geographically widespread, invasive pasture species and demonstrate the general need for targeted, habitat‐ and pathosystem‐specific studies prior to the process of tiered risk assessment.