The temporal dynamics of biotic communities have been widely examined by ecologists. However, systematic reviews on how habitat features, sampling and data evaluation influence temporal patterns are rather sporadic. Here, we reviewed 307 peer‐reviewed scientific articles to characterize the methods and the approaches, as well as to identify the knowledge gaps in the assessment of the temporal dynamics of freshwater fish assemblages with special regard to their stability patterns. The number of publications increased exponentially over decades. We revealed a highly uneven distribution of the studies among continents and ecosystems with a dominant number of papers derived from North America and Europe, and from lotic systems, especially. We also found large variability among studies even within similar habitat types in the examined spatial and temporal scales, sampling methods used, examined assemblage attributes, potential stressors and data analyses. Several knowledge gaps, such as the limited number of large‐scale studies, the insufficient knowledge on the long‐term dynamics of early life history stages and on trait‐based assemblage organization, were highlighted. For enabling meaningful comparisons of fish assemblage dynamics in space and time, further developments in standardization procedures are needed across sampling and data evaluation possibilities. Publicly accessible long‐term data sets with more details on sampling and environmental parameters would also be critically important to determine the effect of a variety of factors on the stability vs. variability of fish assemblages.