Freshwater input is thought to be a critical factor influencing estuaries through multiple direct and indirect pathways. In this study, findings of a key 1992 paper on Apalachicola Bay oyster fishery data and Apalachicola River discharge data from 1960 to 1984 were recreated, and the analysis extended to 1987 to 2013, to evaluate whether relationships previously reported between river discharge and oyster fishery catch per unit effort (CPUE) persist. The originally reported relationship between low river discharge and lower oyster landings 2 y later was confirmed, but when these same relationships for data from 1987 to 2013 were examined, correlation coefficients relating river discharge metrics to oyster fishery CPUE that were significant with 1960 to 1984 data did not persist with data from 1987 to 2013. Combining all available data (1960 to 2013, excluding 1985 to 1986), previously reported significant correlation coefficients were found to have generally persisted or strengthened and the total number of significant correlations increased. A surprising result is the general lack of association between river discharge and oyster fishery landings from 1987 to 2013, a period of frequent drought and generally lower annual river discharge compared with 1960 to 1984. There are multiple possible explanations for the observed relationships between river discharge and oyster fishery landings including (1) counterintuitive changes in oyster fishery landings due to a change in reporting requirements between the two epochs, (2) hyperstable relationship between oyster abundance and fishery CPUE, (3) failure of the Apalachicola Bay oyster population to recover after Hurricane Elena, and (4) ecosystem changes possibly related to nonstationary river discharge levels altering Apalachicola River or Bay ecosystem dynamics in unknown ways. The absence of simple relationships between freshwater input and oyster fishery responses complicates ongoing management and restoration decisions for Apalachicola Bay, and this work demonstrates that, even within the same system, the relationship between freshwater discharge and response by a key estuarine ecosystem constituent is uncertain.