The New England and Mid‐Atlantic regions of the Northeast United States have experienced climate‐induced increases in both the magnitude and frequency of floods. However, a detailed understanding of flood seasonality across these regions, and how flood seasonality may have changed over the instrumental record, has not been established. The annual timing of river floods reflects the flood‐generating mechanisms operating in a basin, and many aquatic and riparian organisms are adapted to flood seasonality, as are human uses of river channels and flood plains. Changes in flood seasonality may indicate changes in flood‐generating mechanisms, and their interactions, with important implications for habitats, flood plain infrastructure, and human communities. I applied a probabilistic method for identifying flood seasons at a monthly resolution for 90 Northeast U.S. watersheds with natural, or near‐natural, flood‐generating conditions. Historical trends in flood seasonality were also investigated. Analyses were based on peaks‐over‐threshold flood records that have, on average, 85 years of data and three peaks per year—thus providing more information about flood seasonality than annual maximums. The results show rich detail about annual flood timing across the region with each site having a unique pattern of monthly flood occurrence. However, a much smaller number of dominant seasonal patterns emerged when contiguous flood‐rich months were classified into commonly recognized seasons (e.g., Mar–May, spring). The dominant seasonal patterns identified by manual classification were corroborated by unsupervised classification methods (i.e., cluster analyses). Trend analyses indicated that the annual timing of flood‐rich seasons has generally not shifted over the period of record, but 65 sites with data from 1941 to 2013 revealed increased numbers of June–October floods—a trend driving previously documented increases in Northeast U.S. flood counts per year. These months have been historically flood‐poor at the sites examined, so warm‐season flood potential has increased with possible implications for aquatic and riparian organisms.