Anthropogenic impacts as environmental degradation and fisheries have been historically associated with changes in structure and dynamics of fish assemblages. A fundamental requisite to evaluate such man-induced changes on fish assemblages is the analysis of long-term time series that allow factoring out inter-annual and decadal natural variations in physical and biotic factors. Based on a standardized monthly long-term database (1997-2012) of experimental fish collections at shallow waters of estuarine and adjacent surf-zone areas of sub-tropical coastal lagoon in southern Brazil (32ºS-52ºW), we evaluated long-term trends in fish abundance and diversity and their correlates with fisheries and environmental factors. Overall species composition and species richness (S) at both estuarine (95) and surf-zone (54) were quite similar across years (similarity=52.1 ± 5.8 SD), but there was high inter-annual variability correlated with local (temperature, salinity), regional (precipitation) and global (ENSO) factors. In the estuary, species richness decreased substantially between 2002 (S=45) and 2012 (S=22), and there were marked variability in abundance across years (CPUE mean =92.3; Min=34.5; Max=163.4). A contrasting pattern was observed at the surf-zone, with lower inter-annual variation in species richness, a marked decrease in fish abundance (CPUE mean=101.9; Min=31.3; Max=221.5). Bayesian generalized additive models (GAMs) corroborate with those results and revealed a decrease in both species richness and abundance of both estuarine and adjacent surf-zone areas. Environmental conditions explained only partially the observed inter-annual and decadal variability in both estuarine and marine fish assemblages. Man-made changes associated with habitat loss and increasing fishing pressure could be responsible by some of long-term variations observed in these fish assemblages.