Phytoplankton account for at least half of ecosystem primary production in coastal waters and support a bulk of marine food webs and strongly influence biogeochemical cycling. Changes in phytoplankton communities often precede changes in ecosystem function. In this chapter, a phytoplankton model, using CHEMTAX software, was developed to evaluate seasonal and spatial dynamics of the phytoplankton abundance and community composition in a case study of Port Lincoln off coastal waters of South Australia. It aims to increase understanding and knowledge of seasonal and interannual dynamics of phytoplankton community in coastal waters and implications for marine ecosystem health and sustainable fisheries and aquaculture development.