Abstract Although the scale-dependence of ecological patterns and processes is recognized by freshwater ecologists, current knowledge of scale effects is rudimentary and non-quantitative. We review issues of spatial and temporal scale in this paper to highlight conceptual problems relating to scale and some potential solutions. We present examples of how the spatial scale of a study influences observed patterns and their interpretation, and discuss how the size of an experimental arena influences the degree to which the dynamics of studied populations are influenced by exchange processes (immigration and emigration). The results of small-scale field experiments in streams will often be strongly influenced by the per capita exchange rates of organisms and differences in exchange rates may explain differences in the perceived effects of stream manipulations across scales. Spatial extent also influences the amount of spatial heterogeneity within a study site or arena, with important consequences for the outcome of predator-prey interactions. We suggest that changes in the availability of prey refuges may help explain why predator manipulations in streams appear to weaken as arena size increases. We also recommend that new techniques for decomposing and quantifying spatial heterogeneity be applied to characterize scale-dependent variation in freshwater systems. Lastly, we discuss the pitfalls of mismatching the temporal scale of experiments and models. Models incorporating spatial heterogeneity and the behaviour of organisms are needed to predict the short-term outcome of perturbations in streams, whereas models predicting long-term dynamics will need to integrate the impacts of episodic disturbance and all life history stages of organisms. In general, we recommend that freshwater ecologists undertake more multi-scale sampling and experimentation to examine patterns and processes at multiple scales, and make greater attempts to match the scales of their observations and experiments to the characteristic scales of the phenomena that they investigate.