Paleoecological techniques are useful tools to identify restoration targets and natural variability for natural resource management programs. However, despite recent advances, caution is required when employing paleoecological techniques in estuaries, due to their dynamic nature relative to lake environments where these techniques were pioneered. This study used a novel combination of chronological, diatom, geochemical and isotopic data to assess the effectiveness of using these techniques in estuaries, and to develop an understanding of environmental changes within Moreton Bay, an open estuarine environment in subtropical east Australia. Results indicated mixed success, with 210Pb results indicating only background unsupported 210Pb levels, 14C results indicating sediment deposition from mixed sources, no diatom preservation and inconsistencies between geochemical and isotope proxies. Evidence did exist that the Moreton Bay sediments have been derived from different sources over the past 10 000 years. However, isotope records were not able to identify the likely sources of these sediments. Problems with diatom preservation were most probably due to the high salinity and temperatures associated with subtropical open embayment estuaries. Future studies attempting to identify environmental histories of estuaries should incorporate river-influenced locations rather than marine-dominated sites to ensure better diatom preservation and more definitive geochemical signals.