Impacts of land-use on estuarine environmental parameters and nutrients are well documented, but little is known about these characteristics during extensive periods of low water flow (i.e., drought). Droughts are set to increase in frequency and magnitude with climate change, and understanding their influence on ecosystems is imperative. We investigated differences in environmental parameters and nutrients in urban and rural estuaries during a period of prolonged low flow. Sampling was done along each estuary at multiple times to place small-scale variability in the context of land-use differences. No differences were detected between land-use for environmental parameters or nutrients in mean effects or variance structure. Urban estuaries had reduced variation in nutrients over time compared to rural estuaries, which suggested that their concentrations are more stable. Large differences existed within and between individual estuaries, and over time. Low freshwater flow conditions in estuaries provide a glimpse to future climate change impacts of drought, and a baseline upon which pollution and anthropogenic effects can be assessed.