The earliest eukaryotes recorded in continental environments are non-pollen palynomorphs (NPP) in Mesoproterozoic strata, and NPP provide our best insights into lacustrine ecosystems through the Paleogene. They have been underexploited in studies of younger lake sediments, either ignored or only qualitatively observed, because many NPP are destroyed by standard processing techniques for pollen and embryophyte spores. The palaeoenvironmental potential of palynomorphs, with representatives from all eukaryotic kingdoms as well as cyanobacteria and from all trophic levels in various lacustrine environments, has been recognized by a few Quaternary palynologists in the past few decades. NPP have proven particularly valuable in archaeological and environmental monitoring studies of human impact on freshwater ecosystems, with spores of some fungi and eggs/egg cases of some flatworms and roundworms associated with faeces of humans and livestock, and the acid-resistant remains of various life stages of cyanobacteria, algae and their aquatic consumers responding to increased turbidity and nutrient influx associated with permanent human settlements, particularly those associated with agricultural activity. Descriptions of NPP commonly encountered in Quaternary lake sediments and case studies illustrating applications to various research questions should encourage more palynologists that ‘“Quaternary non-pollen palynomorphs” deserve our attention!’, to quote Prof. Bas van Geel (2006, Review of Paleobotany and Palynology, 141, vii–viii, https://doi.org/10.1016/j.revpalbo.2006.04.001), undisputed Father of NPP research.