Using the Bay of Biscay (BoB) as a case study, we conducted a transnational assessment of the mean trophic level (MTL, Ospar FW4) indicator at sub-regional level, over the last three decades. Our results confirm the apparent recovery of BoB’s bentho-demersal system, as shown by trends in the MTL indicator based on survey data. However, they also point at a concomitant “fishing through” process where the apparent stability revealed by the MTL indicator based on landed catch data may be masking the expansion of demersal fisheries to deeper waters, and an over-exploitation of resources (particularly abundant pelagic species). Moreover, they show how the combined examination of independent surveys and fishery landings allows the identification of ecological trends in ecosystem studies. In addition, our results confirm that analysing MTL at various threshold levels helps discerning the causality of trends in this indicator, especially if analyses for pelagic and demersal species are run independently. Further studies, at smaller (i.e. local) spatial scales, need to be conducted to ascertain our results and suggest appropriate management strategies aimed at regulating fisheries expansions in the area.