We examine among- and within-catchment variability in century-long patterns of phytoplankton abundance and sedimentary C and N isotopic content in two temperate oligotrophic estuaries of the Eastern Canadian Coast. Two upstream sites are compared with one downstream site within a large, relatively unimpacted catchment. The downstream site is compared to another site situated in an adjacent catchment that experienced more urban development. Variations in δ13C, δ15N, and organic content in downstream sites coincided with either water flow restriction events following bridge construction in the 1950s, or wastewater treatment plant startup in the 1960s. Furthermore, downstream sites showed algal abundance peaks between the 1920s and 1990s, in contrast to the upstream site where algal abundance increased throughout the twentieth century. We then quantified the relative importance of two sets of environmental factors as correlates of phytoplankton abundance and composition. We show that downstream algal communities (especially cryptophytes and cyanobacteria) were influenced by land-use factors. In contrast, upstream algal communities were more influenced by climatic variables, namely August air temperature rather than land-use change (e.g., pig farm, golf course). We propose that sand-bar built estuaries tend to be more sensitive to land transformation events at downstream reaches, where land-derived materials tend to accumulate. In contrast, upstream reaches of estuaries drain relatively smaller surface areas, making them potentially more sensitive to climatic signals. © 2021, Coastal and Estuarine Research Federation.