BACKGROUND: The present study investigated the changes in swimming speeds and sex differences for elite male and female swimmers competing in 5 km, 10 km and 25 km open-water FINA World Cup races held between 2000 and 2012. METHODS: The changes in swimming speeds and sex differences across years were analysed using linear, non-linear, and multi-level regression analyses for the annual fastest and the annual ten fastest competitors. RESULTS: For the annual fastest, swimming speed remained stable for men and women in 5 km (5.50 ± 0.21 and 5.08 ± 0.19 km/h, respectively), in 10 km (5.38 ± 0.21 and 5.05 ± 0.26 km/h, respectively) and in 25 km (5.03 ± 0.32 and 4.58 ± 0.27 km/h, respectively). In the annual ten fastest, swimming speed remained constant in 5 km in women (5.02 ± 0.19 km/h) but decreased significantly and linearly in men from 5.42 ± 0.03 km/h to 5.39 ± 0.02 km/h. In 10 km, swimming speed increased significantly and linearly in women from 4.75 ± 0.01 km/h to 5.74 ± 0.01 km/h but remained stable in men at 5.36 ± 0.21 km/h. In 25 km, swimming speed decreased significantly and linearly in women from 4.60 ± 0.06 km/h to 4.44 ± 0.08 km/h but remained unchanged at 4.93 ± 0.34 km/h in men. For the annual fastest, the sex difference in swimming speed remained unchanged in 5 km (7.6 ± 3.0%), 10 km (6.1 ± 2.5%) and 25 km (9.0 ± 3.7%). For the annual ten fastest, the sex difference remained stable in 5 km at 7.6 ± 0.6%, decreased significantly and linearly in 10 km from 7.7 ± 0.7% to 1.2 ± 0.3% and increased significantly and linearly from 4.7 ± 1.4% to 9.6 ± 1.5% in 25 km. CONCLUSIONS: To summarize, elite female open-water ultra-distance swimmers improved in 10 km but impaired in 25 km leading to a linear decrease in sex difference in 10 km and a linear increase in sex difference in 25 km. The linear changes in sex differences suggest that women will improve in the near future in 10 km, but not in 25 km.