Distribution, frequency and intensity of harmful phytoplanktonic species are impacted by changes in environmental conditions. In the Bay of Brest, Alexandrium minutum has been responsible for several harmful algal blooms (HABs) associated with toxin production causing paralytic shellfish poisoning (PSP). Additionally, Lepidodinium chlorophorum causes green water and hypoxia locally in the Bay of Biscay. Previous studies revealed that L. chlorophorum’s success was related to possible competitive exclusion. Therefore, the phytoplankton composition and the environmental conditions should be taken into account. This study aims to assess the combined effect of changes in habitat conditions and community structure with the occurrence of HAB species, on a spatial-temporal scale. For the investigation we first used the Hutchinson’s niche concept by means of the Outlying Mean Index (OMI) analysis. The OMI analysis enable us to observe the environmental variables defining the ecological niche of the harmful species among the community. Secondly, we used the subniche theory to highlight the environmental variables defining the subniches in cases of high and low abundance of HABs with an estimation of the biological constraint restricting the species’ subniche. This was undertaken using the Within Outlying Mean indexes (WitOMI) calculated under environmental conditions promoting high (H) and low (L) abundance bloom. Thirdly, we used the Indicator Species Concept from the Indicator Species Analysis (ISA) to link the biological restriction with potential competing or indicator species. We combined a data set from the French National Phytoplankton and Phycotoxin Monitoring Network (REPHY), the Velyger network (oyster monitoring program) and satellite imagery. A total of 44 stations, over the period of 1998–2017 using 50 taxonomic units. 36 taxa had significant niche and were mostly distributed along nutrient and salinity gradients. The two species of interest L. chlorophorum and A. minutum seemed to have similar affinity for summer-like environmental conditions and both used a marginal habitat compared to the rest of the community. A. minutum had a larger niche due to a greater affinity to the estuarine-like conditions. The subniche of the two species had a similar response to the environmental variation; their respective abundance was partly caused by greater environmental restrains. Their success in abundance appeared to be linked to local hydrodynamics which increases or reduces resources. On the other hand, the biotic pressure exerted upon A. minutum and L. chlorophorum were antagonistic. A possible competitor assemblage was exposed but the analysis was inconclusive. The methodological limitations were discussed as well as a perspective for future similar studies.