We present an integrative statistical approach for estimating the current conditions of marine-bird habitats affected by human activities. We first estimated the influence of multiple human offshore activities on the species of interest using integrative regression techniques. We then used these models to predict the distribution and abundance of the species throughout the study area, in both the current situation, with human activities, and in a hypothetical situation without the effects of the studied human activities. We finally developed different measures related to the comparison between these two scenarios. The presented approach allows the integration of bird-count data from different sources and sampling schemes, thus maximizing the underlying database. It also provides a local metric highlighting critical regions where locally high abundance is co-localized with large declines in abundance due to human activities, as well as a global metric quantifying the overall condition of the marine-bird habitat in the study area in relation to human disturbance. This approach allows us to assess the cumulative influence of several anthropogenic pressures. We exemplarily applied the above approach to four different species and two different sea regions, namely European herring gulls and long-tailed ducks in the German section of the Baltic Sea, and European herring gulls, red-throated loons, and common murres in the German–Dutch–Belgian part of the North Sea. The considered activities were offshore wind farms, bottom-trawling fishery, and ship traffic. The results confirmed the avoidance of and attraction to human activities by marine bird species found in previous studies. These results show that the methods developed here can be used to provide indicators for inclusion in bird assessments under OSPAR and HELCOM conventions, and MSFD Article 8, criterion D1C5 (habitat for the species). The resulting indicator can be used to inform programmes of measures under MSFD Article 13.