This study examined scientific papers published in authoritative international journals authored by researchers working on South African estuaries between 1949 and 2020. Publications indexed in Web of Science and Scopus were analysed for bibliometric indices, such as number of papers, most cited papers, most prolific authors, and leading countries and institutions, using RStudio and VOSviewer. A total of 1470 documents were retrieved from hybrid databases covering 1404 authors and 309 literature sources with an average document/author ratio of 1.05 and author/document ratio of 0.96. The number and years of publications fitted into polynomial function and other statistical models suggesting increased output in future. Researchers collaborated mostly with European countries, specifically Belgium, UK, Netherlands, Sweden, Spain, France, Germany, Norway, Italy and Austria. Coastal research institutions were more prolific with Nelson Mandela University in Port Elizabeth occupying the top spot with 323 articles. Based on thematic literature classification, 20 research domains were identified with most studies featuring fish (n = 346, 23.5%), geography/geology (n = 231, 15.7%), and phytoplankton (n = 198, 13.5%). Temporal keywords analysis showed that studies focused mostly on the St Lucia, Swartkops and Knysna estuaries. Topical themes emerging from this review can be used to guide future research towards neglected areas and strengthen collaboration between authors from allied disciplines.