The concepts that have received considerable attention by researchers and that have guided trends in the interpretation of research results relevant to CalCOFI can be organized according to the temporal scales that they encompass, notably the decadal (10–100+ years), inter-annual (1–5 years), seasonal (1 month to 1 year) and weather (less than 1 month) scales. At the decadal scale are regime shifts, the basin hypothesis of range contraction and expansion, cycles in fish and plankton assemblages, the alternation of dominance in small pelagic fish populations, and geographical shifts of assemblages with secular trends in climate. Inter-annual scales are dominated by the effects of El Niño-Southern Oscillation events and by mesoscale variability and associated advection. At seasonal scales, I discuss upwelling and production, the spring transition and phenology, the optimal environmental window concept, fish migration, and variability in small pelagic fish spawning habitat. At the shortest daily to weekly time frames, or weather scale, the key concepts include mixing, stability and recruitment, mortality and patchiness.