Many monitoring programs aim to understand regional biodiversity patterns in relation to global and regional conservation targets, using either community-wide biodiversity metrics to describe the community status or trends of pre-selected “key” species as biodiversity change indicators. However, the former often lacks information on which species are changing, and the latter is heavily skewed towards specific taxa, potentially overlooking changes in other, functionally important taxa. We gathered an extensive set of monitoring data with over 3000 population trends (ranging from 5 to 91 years in duration) for a wide range of taxa across the Wadden Sea. We combined a systematic and quantitative categorization of population trends (weighted vote count) with a meta-analysis on different taxonomic levels. This allowed the first cross-taxa synopsis of species declines and increases and determined their directionalities throughout time. Our meta-analysis showed an overall decrease in population size for fish, zooplankton, and plant species, while birds showed an overall increase. However, these increases mask recent negative trends within specific bird groups since the late 1990s. In contrast, fish populations exhibited declines over the entire monitoring period. Species with declining populations (losers) were phylogenetically related, whereas species with increasing populations (winners) represented various organismal groups. Directionality and onsets of change in population trends were temporally synchronized throughout several groups, such as bivalves, fish, and birds, and may provide warning signals for future local extinctions in these taxa. Our analysis moves beyond typical indicator species by including the entire species inventory of the system. Basal trophic levels of aquatic ecosystems, such as zooplankton and phytoplankton, are often missing from policy assessments but are among the most important organism groups for ecosystem functioning. Here, we show that without additional monitoring effort, a systematic analysis of population trends adds to our understanding of trophic and compositional restructuring of ecosystems.