The implementation of food web criteria in the Marine Strategy Framework Directive context faces several difficulties, namely the lack of data for relevant taxa, the absence of operational indicators, and spatially and temporally limited datasets. This work aims to identify ecologically relevant scales in the Celtic Seas (CS) and the Bay of Biscay and Iberian Coast (BBIC). Four food web criteria—mean trophic level (MTL), mean trophic level with cut-offs (MTL_3.25 and MTL_4), large fish indicator (LFI) and mean abundance across trophic guild (MATG)—were assessed using groundfish data and tested using generalized additive models, for six spatial scales and four temporal scales. In both subregions, MTL required yearly and locally defined assessment scales. As for MTL_3.25, it improved significantly when downsizing spatial scales but was temporally consistent. In the CS, locally defined scales and yearly data explained MTL_4 and LFI. While in BBIC, MTL_4 and LFI patterns were defined spatially by region and depth and temporally by year. MATG variability was unaffected by scales. Using the scales identified, food web criteriawere assessed for the Portuguese continental waters. Criteria failed to achieve Good Environmental Status in areas of the Southwest and South of Portugal. Although downsizing scales revealed that criteria were below the threshold at local/regional level, differences in classification are expected to be limited if spatial assessments are aggregated.