Long-term environmental records are among the most valuable assets for understanding the trajectory and consequences of climate change. Here we report on a newly recovered time-series from Project Oceanology, a non-profit ocean science organization serving New England schools (USA) since 1972. As part of its educational mission, Project Oceanology has routinely and consistently recorded water temperature, pH, and oxygen as well as invertebrate and fish abundance in nearshore waters of the Thames River estuary in eastern Long Island Sound (LIS). We digitized these long-term records to test for decadal trends in abiotic and biotic variables including shifts in species abundance, richness, and diversity. Consistent with previous studies, the data revealed an above-average warming rate of eastern LIS waters over the past four decades (+0.45 °C decade−1), a non-linear acidification trend twice the global average (−0.04 pH units decade−1), and a notable decline in whole water-column dissolved oxygen concentrations (−0.29 mg L−1 decade−1). Trawl catches between 1997 and 2016 suggested a significant decrease in overall species diversity and richness, declines in cold-water adapted species such as American lobster (Homarus americanus), rock crab (Cancer irroratus), and winter flounder (Pseudopleuronectes americanus), but concurrent increases in the warm-water decapod Libinia emarginata (spider crab). Our study confirmed that Long Island Sound is a rapidly changing urban estuary, while demonstrating the value of long-term observations made by citizen-scientists, educators, and other stakeholders.