Results from previous bioassays conducted in the oligotrophic Atlantic Ocean determined availability of inorganic nitrogen (N) as the proximal limiting nutrient control of primary production, but additionally displayed a synergistic growth effect of combined N and P addition. To classify conditions of nutrient limitation of coastal phytoplankton in the tropical ocean, we performed an 11-day nutrient enrichment experiment with a natural phytoplankton community from shelf waters off Northwest Africa in shipboard mesocosms. We used pigment and gene fingerprinting in combination with flow cytometry for classification and quantification of the taxon-specific photoautotrophic response to differences in nutrient supply. The developing primary bloom was dominated by diatoms and significantly higher in the treatments receiving initial N addition. The combined supply of N and P did not induce a further increase in phytoplankton abundance compared to high N addition alone. A secondary bloom during the course of the experiment displayed again higher primary producer standing stock in the N-fertilized treatments. Bacterial abundance correlated positively with phytoplankton biomass. Dominance of the photoautotrophic assemblage by N-limited diatoms in conjunction with a probable absence of any P-limited phytoplankton species prevented an additive effect of combined N and P addition on total phytoplankton biomass. Furthermore, after nutrient exhaustion dinitrogen (N2) fixing cyanobacteria succeeded the bloom-forming diatoms. Shelf waters in the tropical East Atlantic may thus support growth of diazotrophic cyanobacteria such as Trichodesmium sp. subsequent to upwelling pulses.