The Marine Strategy Framework Directive is undergoing its second implementation cycle while work is ongoing to promote further harmonization, especially regarding the European Commission standards on datasets, metrics, and thresholds. Even though spatial scales for Biodiversity descriptor criteria concerning fish are set by the Directive at subdivision of region, subregion or region level (depending on the fish species group), the scales of the assessment have never been confirmed across the multiple metrics, taxons and regions. In this work, Descriptor 1 – Biodiversity and Criterion 2 – Population abundance of the species (D1C2) was evaluated and compared for six non-commercial fish species, at five geographical scales in the Portuguese Continental waters, to understand if scales used in the assessment affect species group status and hinder the establishment of adequate monitoring or management measures. For comparability purposes, the methods used were identical to the MSFD; a Breakpoint analysis combined with a Trend analysis of the last five years. Results showed that assessments at Portuguese continental Economic Exclusive Zone level mask local population patterns that were visible when smaller size scales were used, and that each species had different scale requirements. Argentyna sphyraena had low biomass index in the northern region of Aveiro, and species analysed in the Algarve region presented distinct patterns. Downsizing scales revealed that Microchirus variegatus was not in good status – i.e., below threshold - in the southern coastal area, requiring further attention to understand how pressures are impacting populations locally. Although the overall status of the species was maintained, when species assessment was integrated, smaller sized assessment scales are required to understand how populations respond to pressures locally and therefore how monitoring and management of status and pressures should be implemented. Results highlight the need to consider species biology, ecology and population dynamics to define precise scales of assessment and to identify areas of risk at locally relevant scales.