Benthic diatom assemblages were collected from 52 wetlands on Cape York to investigate sensitivities to environmental attributes and subsequently develop inferential models. Strong and consistent relationships between total alkalinity, bicarbonate concentration, pH, electrical conductivity and latitude and the diatom community were identified and these were considered for development of models. Rivers in Cape York have a general east to west orientation and it was assumed that latitude was potentially representing biogeographic differences between rivers. A multivariate statistical comparison of diatom assemblages between river basins showed significant differences; however, there was substantial overlap in species composition. Inference models based on individual diatom species optimal and preferential ranges for each of the other environmental attributes were developed. These models were tested using a comparison of the measured values and the predicted values. All comparative relationships were significant and had low root mean square error. In addition, a dataset for independent testing of electrical conductivity was applied to the transfer function. Results showed good predictions giving confidence in its applicability beyond the training dataset. These models and the understanding of the influence water quality can have on diatom assemblages provides a tool for future application to monitoring programs and palaeoenvironmental investigations of wetlands across Cape York.