Phenology changes are increasingly recognized as a common response of species to ongoing global change. Phenology can be influenced by environmental cues that impact the initiation or duration of life history events as well as intrinsic organismal traits that may affect how different species respond to such environmental cues. Despite the importance of phenology for biodiversity conservation as demonstrated by terrestrial and marine research, freshwater phenology is understudied. Therefore, we conducted a literature review on freshwater phenology research to summarize the spatial, taxonomic and temporal biases of studies; as well as relationships between phenology metrics, environmental cues and intrinsic species traits studied in these systems. We find that phenology research in freshwaters may be limited by a lack of long‐term time‐series data, especially in lotic habitats. Phenology metrics studied differed between lotic and lentic habitats, with limnological research focused on planktonic population growth whereas macroinvertebrate emergence and fish spawning seasons are the most frequently studied aspects of phenology in streams and rivers. Across habitats, temperature is the most investigated environmental cue, with additional research attention to resources and hydrology in influencing phenology events in lentic and lotic environments, respectively. Knowledge gaps in contemporary freshwater phenology research include relationships between phenology and environmental cues in tropical systems, understanding of non‐salmonid fish phenology and testing hypotheses related to intrinsic traits. We recommend that future research broaden the biological, spatial and temporal scales of phenology studies in these systems, and make use of novel data sources, methods and technologies to address contemporary research gaps.