Within the legal frameworks regulating post-market monitoring (PMM) of genetically modified (GM) crops, both notifier and regulatory authorities have to decide whether an observed environmental effect is relevant, i.e., whether the effect is considered to represent an environmental damage and therefore requires corrective action.   Given that presently there is no consensus on applicable criteria to valuate 'environmental damage', notifier and regulatory authorities are facing a number of challenges when being confronted to environmental decision-making related to PMM of GM crops.   In the present paper, we argue that these challenges mainly have two causes.   First, there are methodological limits in data collection and analysis, which in turn challenge decisions whether the observed effects fulfill the proposed criteria for environmental damage.   Second, scientific data is valued controversially due to differing value judgement on the environmental entities that should not be affected by the cultivation of GM crops.  We analyse both challenges and propose potential perspectives how they could be addressed.