Environmental Economic Accounts track the supply and use of interconnected ecosystem services, to inform environmental decision makers about the past and current status of ecosystem services. Ecosystem services are underpinned by the extent and condition of ecosystems, both of which are tracked in accounts with indicators. Policy makers need to know if indicators lead or lag environmental change, so that indicators are interpreted appropriately. Here we test the United Nations System of Environmental-Economic Accounting-Ecosystem Accounting (SEEA-EA) framework for ecological condition to ask whether interconnected indicators lead or lag long-term change in ecosystem condition. We chose a case-study with high variability, which likely confounds our ability to track long-term change- a catchment in Northern Australia with high year-to-year variation in river flow that leads to high natural variation in ecological condition. We first quantified covariation among ecological indicators for pasture biomass, vegetation greenness and barramundi catch per unit effort. Covariation in the indicators was driven by river flow, with higher values of all indicators occurring in years with greater river flow. Barramundi catch per unit effort was most sensitive to changes in river flow, followed by a vegetation greenness and pasture biomass. We then defined reference bounds for each indicator that accounted for natural variation in river flow. We predicted the emergence times for each indicator, the time taken for each indicator to emerge from the background of natural variation. Emergence times were >10 years in all cases. Detecting change was more difficult where there were gaps in data. Ecosystem accounts can be used to compare ecological condition against performance objectives, but should consider natural variation in the system. National accounts are often used by decision makers to directly inform near-term actions, because economic indicators respond rapidly to new policies and the prevailing economic conditions. We found that ecological condition indicators in highly variable ecosystems are lagging indicators of change, and as such should be used to assess historical performance, not as leading indicators of future change.