Long-term ecological surveys (LTES) often exhibit strong variability among sampling dates. The use and interpretation of such interannual variability is challenging due to the combination of multiple processes involved and sampling uncertainty. Here, we analysed the interannual variability in ~30 years of species-density (fish and invertebrate) and environmental observation time series in four aquatic-systems (stream, river, estuary, and marine continental shelf) with different sampling efforts to identify the information provided by this variability. We tested, using two empirical methods, whether we could observe simultaneous fluctuation between detrended time series corresponding to widely acknowledged assumptions about aquatic population dynamics: spatial effects, cohort effects, and environmental effects. We found a low number of significant results (36, 9, 0% for spatial, cohort, and environmental effects), suggesting that sampling uncertainty overrode the effects of biological processes. Our study does not question the relevance of LTES for detecting important trends, but clearly indicated that the statistical power to interpret interannual variations in aquatic-species densities is low, especially in large systems where the degree of sampling effort is always limited.