The impacts of habitat modification for mosquito control by runnelling in a sub-tropical salt marsh in eastern Australia were evaluated over 20 years (1985-2005) on a quarterly basis. Runnels are shallow channels that connect isolated pools to the tidal inlet. Differences between the first month and the last were assessed as two snapshots in time and showed a similar nature of change between the two times for treatment and controls, though these were significant only for substrate moisture (higher in runnel samples) and salinity (lower in runnel samples). Over the whole 20 years the impacts at the Coomera site were to reduce mosquito larval populations, with small magnitude impacts on the environment. These were, for the runnel samples compared to controls: increased substrate moisture, lower substrate salinity, less dense and smaller Sporobolus and Sarcocornia, slightly lower and less saline water table and more crab holes. These differences reflected a similar direction of change for both runnel and control samples, in all the variables observed and may be associated with regional land use or climate or sea level changes. During the last 5 years substrate moisture was higher near runnels than controls and this may be a response to drought conditions over this period. The modification has had no maintenance.