Advances in genomic techniques have great potential to accelerate the development of the microalgal sector and to address key challenges related to upscaling. Genetically modified microalgae (GMM) can exhibit enhanced biomass productivity, increased accumulation of valuable biocompounds, or express other beneficial traits compared to their non-modified counterparts. However, the application of GMM and their associated cultivation methods may lead to unintentional release, potentially affecting adjacent ecosystems. Here we apply a problem formulation approach to support the environmental risk assessment of novel GMM relative to their wild-type counterparts. We focus on potential effects on ecosystem services provided by natural microalgae communities. We present plausible pathways to harm through which GMM could exert adverse effects and formulate relevant research questions to evaluate the likelihood of each step within these pathways. Existing knowledge on the hazards associated with invasiveness, gene transfer and toxicity of GMM is compiled and discussed. Together, these elements provide a practical framework for identifying relevant hazards and guiding data generation to support environmental risk assessments of GMM.