Rocky reef temperate mesophotic ecosystems (TMEs) are becoming increasingly acknowledged as important ecosystems globally due to their spatial extent and high biodiversity values. Survey platforms such as autonomous underwater vehicles (AUVs) and remotely operated vehicles (ROVs) are the preferred tool for TMEs as they allow the collection of imagery over large spatial scales and depths. This imagery has led to the recent expansion in descriptions of TMEs, but these are currently limited to a small number of regions globally. Descriptions of temporal changes in biota within TMEs are extremely rare and typically limited to a single site with few repeated surveys. Here we report on decadal-scale changes in TMEs across three Australian Marine Parks (AMPs) in the southeast AMP network using benthic imagery collected using an AUV under the integrated marine observing system (IMOS) benthic monitoring program. Contrary to common assumptions, our research highlights that many of the key biota in TMEs in our region fluctuate significantly in abundance over 5–10-year timescales. These findings have important implications for the ongoing monitoring of the AMP network and TMEs generally, as they provide a baseline of temporal change and aid in the development of appropriate indicators for ongoing monitoring.