Freshwater contamination by the presence of microplastics is an environmental urgent issue, and the few available studies suggest that their ecological effects can be as severe as those observed in marine environments. Apart from the physical effects related to the intake and/or ingestion of microplastics, toxic reactions and stress responses to the release of microplastic hazardous components or toxicants can also be expected. Furthermore, microplastics can act as vectors of hydrophobic persistent organic pollutants, which may lead to synergistic ecological effects. Given the lack of research focused on inland waters, the project ComPET aims to gather scientific data and knowledge on the adverse effects and emergent threats posed by microplastics to freshwater ecosystems. It also intends to mechanistically unravel the stress responses to microplastics additives or their sorbed pollutants after ingestion of microplastics, and explain how natural stressors, such as temperature and salinity, mediate those responses. To achieve this, several parameters will be evaluated at sub-organismal (oxidative stress, membrane composition, cell metabolism, immunological responses, neurotransmission), organismal (e.g. mortality, feeding, locomotion, respiration, growth, and regeneration), population (e.g. reproduction) and at the community level (effects on biomass, detritus decomposition rates and primary production). The simulation of realistic environmental conditions with laboratory and mesocosms experiments (artificial streams), the use of ecologically relevant concentrations of microplastics (type and size), the use of freshwater key-species of different feeding groups (collectors, shredder detritivores and predators), and the assessment of responses at different levels of biological organization will allow an integrative view on the real ecological impact associated with the presence of microplastics. The project ComPET has an experienced team in the field of ecotoxicology, also involved in water quality programs and in innovative technologies for microplastics monitoring and assessment. Its results will provide important scientific evidences for the necessary adaptation of the current management and conservation programs for freshwater environments and its endogenous natural resources, which should include strengthening measures to control and reduce the use, consumption and release of microplastics, and in the definition of remediation strategies.