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Women in doctoral programs in Science, Technology, Engineering and Math (STEM) leave without finishing at higher rates than men and, as with men, turn away from academic and research careers. This qualitative study examines the day-to-day influences on female doctoral students during their third or fourth year in physical science and engineering programs. Ethnographic cognitive interviewing and online incident reports document the specific experiences and reactions of 28 participants over a six-month period. The data were analyzed to identify key incidents, categories and recurring themes. Some incidents contributed to women’s growing sense of competence, recognition and identification of oneself as a scientist. Others fit a model of microaggressions and gender barriers in a predominantly masculine culture. Problems of work-life balance were demonstrated for some women. Incidents generated responses by some participants that they would disengage from a research-intensive career trajectory toward alternate career interests outside of academic research. The findings provide information about the lived experiences of women in doctoral programs and suggest that the metaphor of career pathways may be more useful than pipelines in explaining the direction of women who are advanced doctoral students in research-intensive fields.