We highlight women’s contributions to freshwater ecology by firstly considering the historical context and gender-based barriers faced by women attempting to gain an education and secure research jobs in science over the past 100+ years. The stories of four remarkable, pioneering women in freshwater ecology (Kathleen Carpenter, Ann Chapman, Rosemary Lowe-McConnell and Ruth Patrick) illustrate the impact of barriers, emphasise the significance of their contributions and provide inspiration for the challenges ahead. Women still face barriers to participation in science, and the second part of the paper focuses on a current form of discrimination, which is citation metrics used to measure the ‘quality’ or ‘impact’ of research. We show that arguments that citation metrics reflect research quality are logically flawed, and that women are directly disadvantaged by this practice. Women are also indirectly disadvantaged in ecology because they are more likely to carry out empirical than theoretical research, and publications are generated more slowly from empirical research. Surveys of citation patterns in ecology reveal also that women are less likely to be authors of review papers, which receive three times more citations than do original articles. Unless unfettered use of citation metrics is stopped, research will be damaged, and women will be prominent casualties.