From an ecological and economic perspective a better understanding of the impacts of naturally or anthropogenically induced shifts on marine ecosystems is of fundamental importance for humankind. The Helgoland Roads time series, initiated over five decades ago provides a unique opportunity for the study of such changes in the marine environment and their consequences for the phytoplankton community at the basis of the marine food web. Differences in the long-term development of the physical and chemical environment in combination with a high variation in species-specific responses lead to complex biological response characteristics. Our analysis illustrates the high inherent natural variability regarding, for example, the local expression of hydro-climatic variation. It becomes apparent that the transferability of such interaction processes to larger scales such as the whole North Sea requires caution. Considerable effort is still needed for a better understanding of the regional heterogeneity in environmental variations in the North Sea system. We will describe the long-term shifts observed at Helgoland Roads and discuss factors that might prevent us from making broader assessments as to the biological consequences of regime shifts.