We evaluated connectivity, resiliency, and spatiotemporal variation in fish associations between the Tramandal River estuary (TRE) and the adjacent coast (AC). This was based on intermittent and seasonal data covering a discontinuous 21-year period (1995 to 2016) obtained using a standard beach seine with replicate samples collected at several points. In the TRE (405 samples; 42,987 individuals) 55 species were captured. In the AC (297 samples; 54,295 individuals) 41 species were captured. After data standardization the expected richness of the TRE [E(S) = 18.2] was significantly greater (P < 0.05) than that of the AC [E(S) = 14.4]. The fish association structure and distribution patterns in TRE and AC were dynamic and interconnected but quite different in terms of species composition, especially due to the influence of local salinity. The TRE association was richer in a number of species but numerically dominated by marine estuarine-dependent juveniles. The AC association was represented by a few typical marine species in addition to a couple of estuarine-related transient species who used the surf-zone as a passageway to enter the estuary. Even if there was a higher percentage of common species reported (30 out of 66), the monthly average Jaccard index of similarity (I J = 28%) and the monthly average percent similarity index (I PS = 30%) were low, suggesting that the shallow water functional connectivity between AC and TRE was represented by few species that occur equally in abundance in both environments. Trachinotus marginatus and Mugil liza numerically dominated in the AC and M. liza, Mugil curema, and Atherinella brasiliensis at TRE. Juvenile M liza and M curema added up to >70% of the total individuals sampled in both environments. General linearized models (GLM) revealed that diversity was not influenced by interannual variations, evidencing that juvenile fish assemblage of AC and TRE are resilient through the years. Standardized beach samples are able to reveal long-term fluctuation in shallow estuarine fish communities but without an apparent loss in species composition, richness, and relative total abundance. The only observed interdecadal trend was the reduction in abundance of juvenile M. liza that seemed to parallel the reduction in abundance of the adult fishing stocks in southern Brazil.