Climate change is leading to significant alterations to ecosystems all over the world and some of the resulting impacts on fish and fisheries are now becoming apparent. Estuaries, which are highly susceptible to climate change because they are relatively shallow and in close proximity to anthropogenic stressors, provide habitat to many fish species at a critical time in the life history, after transport and just prior to settlement in nurseries. Despite this, the long-term impacts of climate change on larval fish at this critical location/stage in the life history are not well documented. The larval fish assemblage of a coastal estuary was sampled once per week for twenty-six years at a fixed location in southern New Jersey, USA. We used ordination and regression analysis to evaluate the whole assemblage, individual species/family occurrence, and trends in total density and diversity over that time. The larval fish assemblage changed significantly in response to warming water temperatures. In addition, approximately one quarter of the species/families in the assemblage exhibited a statistically significant trend in individual occurrence over time. Of these, all five of the five northern-affiliated species decreased in occurrence while 18 of 21 southern-affiliated species increased in occurrence. Finally, total fish density and species diversity increased over the course of the study. The non-uniform response of the species/families in this larval assemblage is similar to what has been documented in other studies that evaluated the temporal trend of open ocean juvenile and adult fish assemblages.