We are living in a time of rapid biodiversity loss. Numerous studies have shown that modern extinction rates are higher than pre-human background rates. However, these biodiversity studies almost exclusively focus on large vertebrates: mammals, birds, fish and reptiles. We lack sufficient long-term records for many invertebrate taxa to track biodiversity loss. Aquatic, benthic, calcareous invertebrates, however, have the advantage of leaving a long-term record that can readily be sampled along with living communities. They leave easily-fossilized remains in the form of mineralized skeletons that accumulate in the very same sediments in which they live. These so called “death assemblages” contain an underutilized record for long-term monitoring. Here, we leverage calcareous micro- and macro- faunal remains from three aquatic environments spanning a two-dimensional gradient from freshwater to fully marine and polluted to remediated. We find death assemblages of lacustrine, calcareous microcrustaceans (Ostracoda) faithfully record human impacts, both pollution and remediation, across a fresh to hypersaline environmental gradient today. Death assemblages from calcareous marine, macrofauna (Bivalvia) also faithfully reconstruct temporal variation in human impact encompassing pristine, polluted, and successful remediation. We thus establish that death assemblages can act as useful gauges of changes in community assembly and population structures at local and regional scales which would be impossible with only contemporaneous monitoring of the living communities. These examples demonstrate that death assemblages from easily-fossilized taxa represent an effective tool for environmental managers to establish baselines for conservation targets and identify when community assembly approaches natural conditions in remediated ecosystems, rendering previously unrecognized biodiversity loss visible.