For decades, Lake Junín, a vital Peruvian wetland, has endured pollution from multiple sources. This issue has raised concerns about the state of the lake’s water quality. Here, we studied whether there is a relationship between actual water pollution measurements and culturally perceived environmental pollution through three hypotheses: (i) perception of pollution does not necessarily match with actual pollution, (ii) gender, age, and educational level determine the way environment is perceived, and (iii) pollution perception could be used in a positive way to prioritize environmental management. First, we compiled historical data on lake water quality (1974–2008) and recent (2011) levels of key heavy metals, such as As, Cd, Cr, Cu, Pb, and Zn in the areas surrounding the San Juan de Ondores community to determine whether water quality standards for heavy metals have been exceeded. Second, we surveyed 85 community members (13% of the population) using a semi-structured questionnaire to assess their perceptions of water pollution and collect demographic data. We found that, although the measured water quality does not exceed the Peruvian standards, people living in the area perceive the lake as polluted. This contravenes the general idea of using only water quality measurements to determine levels of pollution without considering the complexity of socio-ecosystems. Age, gender, and education had effects on the pollution perception of surveyed people, in that younger, females, and more educated people had an increased perception of pollution. Overall, the results of this study highlight the disconnection between technical assessments and culturally perceived environmental contamination, emphasizing the need for more nuanced and contextually relevant water quality standards.