The risks of pharmaceuticals and endocrine disrupting compounds (P&EDC) to the environment and human health are a current topic of interest. Hundreds of P&EDC may reach the environment, hence, there is a need to rank the level of concern of human exposure to these compounds. Thus, this work aimed at setting a priority list of P&EDC in Brazil, by studying their occurrence in raw and drinking water, calculating health guideline values (GV), and estimating the risks of population exposure to water intake. Data on the Brazilian pharmaceutical market as well as published data of the monitoring of Brazilian natural and drinking water have been collected by means of an exhaustive literature review. Furthermore, many foreign data were also collected to enable a comparison of the values found in Brazilian studies. A list of 55 P&EDC that have the potential to be found in Brazilian water is proposed, and for 41 of these a risk assessment was performed by estimating their margin of exposure (ME), by considering their occurrence in drinking water, and guideline values estimated from reported acceptable daily intake (ADI) data. For seven compounds the risk was deemed high (three estrogens and four anti-inflammatories), whereas for another seven compounds, it was regarded as an ‘alert’ situation. Although such risk analysis is conservative, since it has been calculated based on the highest reported P&EDC concentration in drinking water, it highlights the need to enhance their monitoring in Brazil to strengthen the database and support decision makers. An analysis of the occurrence of antimicrobial resistance agents (antibiotics, resistant bacteria, and resistance genes) in surface waters was also carried out and confirmed that such agents are present in water sources throughout Brazil, which deserves the attention of policy makers and health agents to prevent dissemination of antimicrobial resistance through water use.