Groundwater science has a well-known relationship with social issues when dealing with risk assessment, yet there is a lack of case studies on the topic. Here, we present reflections for dealing with two ethical challenges: (i) the access and use of public domain monitoring data and (ii) the dissemination of scientific research data and its controversial character. The case study is a long-term collaborative research project aiming to bridge the social and natural sciences to tackle ethical questions and their implications for technical reporting and scientific production in a highly contaminated area situated in Portugal. The method included comprehensive interviews with hydrogeologists within the common project, the consulting of documents and the collaborative analysis of situations in online meetings between sociologists and hydrogeologists. The interviews and formal discussions were recorded, transcribed and analysed. In the two cases related to groundwater assessment in contaminated areas we found that researchers refer to emotions and moral dilemmas when they come into regular contact with social actors. Results also show that a different kind of knowledge is produced in these cases and point to three types of researchers’ positionality. The significance of this paper is to encourage reflection and action on ethical issues in the scientific community and specifically in geoethics. Bringing researchers together to share their practice will help to disentangle some of the negative emotions and moral dilemmas of scientific practice and increase the attention researchers pay to other people’s points of view and interests so as to improve the robustness of scientific data.