After setting up a lab at the Hopkins Marine Station, Roughgarden sought to extend her approach of combining theoretical with field research by studying intertidal acorn barnacles (Balanus and Chthamalus spp). Earlier work by Joseph Connell, Bob Paine and others had suggested that the characteristic zonation of rocky intertidal communities was predominantly structured by predation, (for example by Pisaster seastars) and by competition, wherein dominant Balanus species displaced Chthamalus species to the high intertidal zones. Together with her student, Steve Gaines, Roughgarden showed that these interspecific interactions were most important in intertidal localities and communities with a high density of barnacles, such as those Connell and others had studied in Scotland. At Hopkins in Central California, however, barnacle density was lower, and the amount of free space was best explained by periodic pulses of larval recruitment.  With her student Sean Connolly, she then showed, through both empirical observation and modeling, that a latitudinal gradient in upwelling along the west coast of North America created very dense barnacle recruitment in the north (Oregon and Washington), where upwelling was weak, and very sparse barnacle recruitment in the south (California), where upwelling was strong. This in turn explained why field studies in the north had found interspecific interactions to be important, while her own field studies in the south had found larval recruitment to be most important for structuring intertidal populations. This deft synthesis helped to drive a paradigm shift in marine ecology which emphasized larval dispersal and recruitment dynamics over adult interactions and favored demographic models of populations open to larval recruits from distant localities, which dominated the field during the 1990s.
