Ecosystem services offered by freshwater ecosystems, in the form of natural pools have not been fully realized by the public, which has led to limited attention on the conservation of these pools. This study therefore was conducted to investigate the user preferences for sustainable enhancement of recreational values of natural pools and their immediate environment. A total of 320 local users of natural pools located in Rangala and Nillambe were surveyed as the sample. A Discrete Choice Experiment (DCE) was employed to elicit the preference and user Willingness to Pay (WTP). The Marginal Willingness to Pay (MWTP) for the improvement of recreational values of natural pools was estimated using a conditional logit (CL) model. Outcomes of the WTP disclosed a clear preference hierarchy for various enhancements and contributions. Users were willing to pay Sri Lankan Rupees (LKR) 297.6 to reduce the environmental damage by 50% and LKR 84.4 to raise the community income by 20%. The option to have a higher number of recreational activities was highly valued. Respondents were willing to pay a value of LKR 554.8 per year for the multiple benefits provided by the pool ecosystems. Conclusively, the study suggested that efforts to upgrade these natural pools should prioritise income generation, broadening of recreational activities and environmental conservation, in line with respondents’ inclinations.