Micro-phytoplankton density, genera composition, chlorophyll a concentration, and physico-chemical parameters were investigated at five stations(S1—near the coast; S2 and S4—at the edges of the aquaculture set-up; S3—in the center of the set-up; and S5—nearby patch of corals) in and around a coastal channelbased fish farm. The highest total micro-phytoplankton density(TPD), including diatoms, dinoflagellates and cyanobacteria, was recorded at S3((6.28±2.00)×106 cells/L) followed by S4((5.87±2.81)×105 cells/L), S1((4.92×105±8.70×104) cells/L), S5((3.54×105±5.33×104) cells/L) and S2((2.60±1.14)×105 cells/L). Chlorophyll a and nutrient concentrations were highest at S3 and were positively correlated with TPD. Among the 35 genera documented in this study, Chaetoceros spp. was the dominant diatom while Peridinium spp. was the most dominant dinoflagellate. Very low densities of toxic bloom-forming dinoflagellates were encountered during this study. These results suggest that occurrence of non-bloom densities of micro-phytoplankton, possibly due to the natural flushing of the existing lagoonal channel at the aquaculture site, yielded in little environmental impact and can represent an appropriate sustainable approach for future aquaculture development. Micro-phytoplankton density, genera composition, chlorophyll a concentration, and physico-chemical parameters were investigated at five stations (S1-near the coast; S2 and S4-at the edges of the aquaculture set-up; S3-in the center of the The highest total micro-phytoplankton density (TPD), including diatoms, dinoflagellates and cyanobacteria, was recorded at S3 ((6.28 ± 2.00) × 106 cells / L), S1 (4.92 × 105 ± 8.70 × 104) cells / L and S5 ((3.54 × 105 ± 5.33 × 104) cells / Chlorophyll a and nutrient concentrations were at least at S3 and were positively correlated with TPD. Among the 35 genera documented in this study, Chaetoceros spp. Was the dominant diatom while Very low densities of toxic bloom-forming dinoflagellates were encountered during this study. These results suggest t hat occurrence of non-bloom densities of micro-phytoplankton, possibly due to the natural flushing of the existing lagoonal channel at the aquaculture site, yielded in little environmental impact and can represent an appropriate sustainable approach for future aquaculture development.