Fish stock assessment and sustainable management requires that the whole distribution area of the managed fish stocks is representatively sampled. Along with an increasing demand for renewable energy in Europe, a growing number of areas are allocated for current and future offshore wind farms (OWF). Besides various unknown environmental effects, impacts on different stakeholder activities, such as fisheries, are considered during the implementation process. Scientific interests and tasks are, however, often marginalized. The current ban of commercial fisheries and fisheries monitoring in OWFs, in combination with an increase of OWF areas and habitat alteration within OWFs, might therefore bias the time series of scientific surveys and, thus, fisheries stock assessments. The expected increase in the overlap between OWFs and scientific fish surveys coordinated by the International Council for the Exploration of the Sea (ICES) in the Baltic Sea could result in, depending on the survey, up to 6.6–11.5% of the stations and transects being unavailable for sampling. We discuss the potential consequences for survey time series and stock assessments. Further, we aim to stimulate the discussion about the future of current standard surveys in the context of rapid expansions of OWFs, including the need for adaptations in survey design.