Understanding the perceptions of local residents of and visitors to mountain protected areas in terms of their knowledge of and the value they place on aquatic ecosystems is crucial to assess whether nature management and conservation actions will be accepted. This study analyzed the perceptions of visitors to and local residents of the Aigüestortes i Estany de Sant Maurici National Park and the Alt Pirineu Natural Park, both in the Catalan Pyrenees, in relation to aquatic mountain ecosystems. A 10 question survey was conducted on their knowledge and valuation of aquatic mountain ecosystems. Generalized linear models were applied to the responses, testing users’ resident/visitor status and sociodemographic trends as predictor variables. Residents reported a greater level of knowledge of aquatic ecosystems than visitors, which contrasts with the higher valuation given by visitors. Specifically, young residents reported the lowest knowledge, and older residents valued the ecosystems least. Residents of Alt Pirineu Natural Park valued aquatic ecosystems lowest overall, and women residents valued specific aquatic ecosystems lowest. Respondents also highly valued conservation actions linked to the LIFE+ LimnoPirineus project, although residents placed less value on these than visitors. This study helps to fill a gap in the literature on users’ knowledge and valuation of aquatic mountain ecosystems in protected areas. In addition, it provides helpful background for the development of nature management and conservation actions for mountain protected areas.