The aim of this study was to measure the characteristics and risk assessment of microplastics (MPs) in Cape Town Harbour (CTH) and the Two Oceans Aquarium (TOA) in Cape Town, South Africa from 2018 to 2020. Water and mussel MP samples were analyzed at 3 sites in CTH and TOA, respectively. Microplastics were mainly filamentous, black/grey and 1000–2000 μm in size. A total of 1778 MPs, averaging 7.50 (± 0.6 standard error of the mean, SEM) MPs/unit were recorded. Average MP concentrations were 10.3 ± 1.1 MPs/L in water and 6.27 ± 0.59 MPs/individual or, based on weight, 3.05 ± 1.09 MPs/g soft tissue wet weight in mussels. Average MPs in seawater in CTH (12.08 ± 1.3 SEM MPs/L) was significantly higher (4.61 ± 1.1 MPs/L) than inside the TOA (U = 536, p = 0.04). Various risk assessment calculations indicate that MPs in seawater poses a greater ecological risk than MPs in mussels at the sites sampled.