As a key contribution to Canada's Ecosystem Status and Trends (ESTR) national assessment, the goal of our study was to utilize available flow data as a surrogate of habitat suitability for aquatic ecological communities, and examine temporal trends in hydroecological variables over the 1970–2005 period. Daily flow data were extracted from the Reference Hydrological Basin Network, and an agglomerative hierarchical classification method was used to identify homogenous regions with similar seasonality of the flow regime. Six regime regions were identified reflecting the timing of the annual peaks and low flows in addition to the patterns in the rising and falling limbs. For each of the gauging station sites, the magnitude, duration, timing, frequency, and rate of change of annual hydrological events were quantified through 32 ecologically important hydrological variables. Long-term patterns in the hydroecological variables were quantified using the nonparametric Mann-Kendall trend statistic. The results revealed more trends than would be expected to occur by chance for most variables. Clear regional trend patterns were observed within individual regime groups demonstrating the often differing response to environmental variability within the different regions. Results at the national scale were highly variable, but trends towards increased variability in river flows were observed with a predominant increasing trend in the number of flow reversals over the water year and decreasing trend in the annual low-flow indices. The identified river regime regions offer an initial framework for scientific investigation of hydroecological patterns and an opportunity to move towards a more predictive approach to environmental flows assessment in sustainable resource management and planning. Copyright © 2011 John Wiley & Sons, Ltd.