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The knowledge produced in temperate regions is still used today to evaluate environmental problems in the tropics, without taking into consideration environmental differences, such as local conditions, the sensitivity and ecology of species, and exposure routes of contaminants, essential for understanding and determining the fate and toxicity of chemicals. Considering that Environmental Risk Assessment (ERA) studies for tropical systems are scarce and need to be adjusted, the present study aims at contributing to the awareness and development of tropical ecotoxicology. The estuary of the Paraíba River in Northeast Brazil was selected as a model study-case, as it is a large estuary, subjected to a heavy human pressure due to the numerous social, economic and industrial activities. The present study describes the framework for the problem formulation phase of the ERA process; it first includes a detailed integration of the scientific information available on the study area, to then derive the conceptual model, and finally present the analysis plan for the tier 1 screening phase. The latter is designed to be fundamentally supported by the ecotoxicological line of evidence, to ascertain, without delay, where and why there are environmental problems (i.e., adverse biological effects); ecotoxicological tools developed in temperate climates will be optimized to assess water quality in a tropical system. In addition to its intrinsic value for protecting the study area, the results of the present study are expected to provide an important baseline for conducting ERA in similar tropical aquatic systems across the globe. [Display omitted] • Environmental risk assessments (ERA) in subtropical and tropical countries are still limited. • Contaminants exposure characterization is often studied but toxic effects on biota are not. • In the Paraíba River estuary aquatic biota is particularly at risk due to heavy human pressure. • A retrospective tier 1 (preliminary) ERA for the ecotoxicological line of evidence is proposed. • To spatially map ecological risks, a tier 1 analysis plan with short-term lab tests is derived. [ABSTRACT FROM AUTHOR]