Rapid bioassessment techniques used for aquatic macroinvertebrate and plants in wetlands were tested in New South Wales, Australia. Different options for sampling(mesh size, live-picking times, quadrat size, number of samples or quadrats) and analysis (taxonomic resolution, transformations, biotic indices,multivariate and univariate analyses) are compared to determine optimal sampling effort and evaluate the effects of errors or variability. Applying the data collected in this project to biotic indices that use aquatic macroinvertebrates and plants resulted in the development of indices more appropriate for New South Wales wetlands. The practical outcome of this project is a set of standardised steps to assess wetland quality using biological assemblages. I present protocols that are more appropriate to wetlands and recognise that each protocol would need to be adapted for each wetland type. In conclusion I emphasise the need for scientific rigour in the use of biological indicators and consideration of the effects of errors and implications to sampling designs.