The objective of this study was to assess the distribution patterns of dinoflagellates and ciliates communities during planktonic bloom and post-bloom development periods, in relation to environmental parameters. Their distribution was studied during spring and summer 2012, in coastal waters of Algeria at six sampling stations (four sampling layers). Overall, 116 species were identified, including 98 dinoflagellates. The species richness of microzooplankton was higher in summer (81 species: 67 dinoflagellates, seven tintinnids and seven ciliates) than in spring (76 species: 72 dinoflagellates, three naked ciliates and one tintinnid). Significant difference in total abundances was observed between spring (median = 145 ind l−1) and summer (median = 90 ind l−1) but no significance (P > 0.05, Mann–Whitney test) in Shannon–Wiener (H′spring: 3.31 bits ind−1; H′summer: 3.70 bits ind−1) and evenness (Espring: 0.77; Esummer: 0.84) indices. The ciliate average abundance was higher in summer (11.3 ind l−1) than in spring (1.95 ind l−1), whereas dinoflagellate average abundance was lower in summer (127.92 ind l−1) than spring (190.19 ind l−1). Non-metric multidimensional scaling was used to identify different sample assemblages. It showed that temperature and salinity influenced the distribution pattern in the canonical correspondence analysis followed by chlorophyll a, silicate and nitrate concentrations. Our framework provides insight regarding trait trade off with implications for feedbacks to ecosystems, aiming to bridge the gap of plankton community ecology in Algeria. It elaborates a taxonomic list of dinoflagellates and ciliates in the marine pelagic ecosystem and performs their ecological characterization in their environment.