The present study tested the hypothesis that the exercise protocol (continuous vs. intermittent) would affect the physiological response and the perception of effort during aquatic cycling. Each protocol was divided on four stages. Heart rate, arterial blood pressure, blood lactate concentration, central and peripheral rate of perceived exertion were collected in both protocols in aquatic cycling in 10 women (values are mean ± SD): age=32.8 ± 4.8 years; height=1.62 ± 0.05 cm; body mass=61.60 ± 5.19 kg; estimated body fat=27.13 ± 4.92%. Protocols were compared through two way ANOVA with Scheffé's post-hoc test and the test of Mann- Whitney for rate of perceived exertion with α=0.05. No systematic and consistent differences in heart rate, arterial blood pressure, double product and blood lactate concentration were found between protocols. On the other hand, central rate of perceived exertion was significantly higher at stage four during continuous protocol compared with intermittent protocol (p=0.01), while the peripheral rate of perceived exertion presented higher values at stages three (p=0.02) and four (p=0.00) in the continuous protocol when compared to the results found in intermittent protocol. These findings suggest that although the aquatic cycling induces similar physiologic demands in both protocols, the rate of perceived exertion may vary according to the continuous vs. intermittent nature of the exercise.