The Canary Current has experienced a progressive warming and a decrease in productivity over the last decades. In order to study the effect of stratification in these waters, we conducted a weekly sampling at one station (28°04′N 15°21′E) located ∼3nmi offshore in the 100m isobath, at the edge of the island shelf of Gran Canaria Island (Canary Islands). The sampling was performed over two and a half years, from January 2005 to June 2007, covering the most productive season in subtropical waters, the so-called late winter bloom, three times. The variables measured were temperature, chlorophyll a (Chl a), heterotrophic and autotrophic prokaryotes, pico-, nano-, micro- and mesozooplankton biomass. During 2005, the mixing of the water column started in January, while in 2007 the mixing period was delayed one month. Between years, temperature showed an increase of 0.5°C, and Chl a decreased to half of the initial concentration (from ∼0.50 to ∼0.25mg Chl a m−3). Autotrophic picoplankton and heterotrophic prokaryotes decreased between 2005 and 2007. However, neither nanoflagellates nor microplankton showed this decrease. The mesozooplankton biomass outburst lasted for three months in 2005, two in 2006, and only one month in 2007. Contrary to previously hypothesized size relationships, we did not observe an increase in the contribution of autotrophic picoplankton to total phytoplankton during periods of higher stability of the water column, but the opposite. We explain this surprising finding by possible top-down effects and by the success of motile morphotypes of algae (i.e., small dinoflagellates) under stable, nutrient-limited, conditions. Overall, the results suggest that small inter-annual differences in temperature, resulting in a tendency towards more stratified waters, give rise to important changes in the structure of the pelagic ecosystem in subtropical waters through a combination of bottom-up and top-down effects.