On the basis of 16-yr satellite time series (1987-2003) of sea surface temperature (SST) and using univariate and multivariate statistical techniques, we quantified patterns of fluctuation in oceanographic conditions, as well as their spatial structure along the coasts of South Africa and Chile between 29.0° and 34.5°S. Since variations in environmental conditions over multiple timescales are driven by oceanographic-atmospheric processes modulated by coastal morphology, all of which affect in different ways coastal organisms, we hypothesized that dynamic properties of the environment contribute to characteristic patterns on rocky intertidal biomass structure across upwelling ecosystems. Although long-term mean temperatures were similar between coasts, the relative importance of annual, semiannual, intraseasonal, and high-frequency SST fluctuations differed; South Africa is more strongly pulsed over shorter timescales. Similar spatial discontinuities in thermal regimes were observed, with changes at about 32°S. Multivariate summaries of benthic community structure derived from functional group biomasses revealed striking differences between South Africa and Chile, as well as between regions north and south of 32°S within each ecosystem. Between-continent and regional-scale differences in community structure were largely unrelated to mean SST, but correlated with the different measures of temporal variance in SST. For all functional groups, as well as aggregate measures of benthic community composition, the weekly to annual SST fluctuations explained large fractions (>35%) of biological variability. Results highlight the importance of quantifying the temporal variance of regimes of hydrographic conditions since multispecies assemblages are expected to respond in different ways to the driving oceanographic processes behind these fluctuations.