This work investigates for the first time the seasonal changes in phytoplankton, bacteria, and photosynthetic picoplankton as well as nutrient concentrations on the North-western shelf of Kangaroo Island, South Australia. Seawater samples were collected off Penneshaw desalination plant, where waters from the Investigator Straight, Gulf Saint Vincent and Backstairs Passage meet. Low nutrient values were measured throughout the period of study (July 2012–July 2013) suggesting the occurrence of oligotrophic conditions on the region. The phytoplankton community was dominated by Bacillariophyceae, Dinoflagellata and Cryptophyta. Prochlorococcus Cyanobacteria prevailed among picophytoplankton during most of the period of study (July 2012–July 2013). Previous studies indicate that oligotrophic environments are indeed typically dominated by Prochlorococcus. The dominant species found here seem either adapted to grow under low nutrient concentrations, possessing high surface/volume ratios, or have a mixotrophic behaviour allowing them to complement photosynthesis with predation. This study provides base knowledge on the microbial communities north of Kangaroo Island that is needed to sustain the ecosystem and associated economic activities in the future.