In recent regime shift analyses, the phytoplankton compartment of the marine food web was essentially represented by phytoplankton color or chlorophyll concentration. A detection of changes directly at the species level is highly desirable. The Helgoland Roads data series, a collection of high frequency long-term time series comprising biological and physico-chemical components of the southern North Sea, allow such an investigation at the level of single species. Aiming at a detection and characterization of habitat and community changes in the observation period (1962 until the end of 2008), we selected six species as representatives of certain classes, for example, benthic or neritic species, and applied a combination of novel analysis methods—a fitness-based analysis of the realized niche, a bloom-triggered averaging and a Markovian analysis of co-occurrence and succession patterns—to related abundance time series and concurrent environmental parameter time series. We found a general trend toward enlargement of niche size and shifts of the niche position, interesting salinity patterns around bloom events of two species, and statistically highly significant changes of a phytoplankton community segment after 1965 and after 1998. Interpreting our observations in ecological terms leads to the formulation of testable hypotheses.