Morgan first became drawn into scientific writing when reading popularizers of the savannah hypothesis of human evolution such as Desmond Morris. She described her reaction as one of irritation because the explanations were largely male-centered. For instance, she thought that if humans lost their hair because they needed to sweat while chasing game on the savannah that did not explain why women should also lose their hair as, according to the savannah hypothesis, they would be looking after the children. On re-reading Desmond Morris's The Naked Ape she encountered a reference to a hypothesis that humans had for a time gone through a water phase, the so-called aquatic ape hypothesis. She contacted Morris on this and he directed her to Alister Hardy. Her first book The Descent of Woman (1972) was originally planned to pave the way for Hardy's more academic book, but Hardy never published his book.
Morgan's first publication was mentioned by E. O. Wilson in 1975, comparing it to other "advocacy approaches" such as The Imperial Animal as an "inevitable feminist" counter, but describing the method as less scientific than other contemporary hypotheses. Morgan accepted this criticism and her later books were written in a more scientific tone, or more "po-faced" as she herself described it. As an outsider and a non-scientist she claims to have encountered hostility from academics. Consequently many of her books seem to be written as much to counter the many arguments put forth against the Aquatic Ape Theory as to advance its merits. Her position is summarised in her website. The story of Morgan's quest to have the aquatic ape hypothesis taken seriously was chronicled in the 1998 BBC documentary The Aquatic Ape.
Morgan's version of the AAH has achieved much popular appeal, but has never achieved significant acceptance or serious scrutiny within the scholarly community. The Aquatic Ape Hypothesis was subjected to a full academic symposium in Valkenburg, South Holland in 1987, but the papers were mostly critical of the hypothesis. Despite this, Morgan continued to promote the hypothesis, with invitations to speak at universities and symposia including a TED talk in 2009.