Selenium (Se) concentrations in water column, sediment and insect compartments were measured over 3 years, in conjunction with selected physicochemical parameters, from lotic (flowing water) and lentic (standing water) sites within a single watershed in Utah, USA. There was evidence for steady-state concentrations of total [Se] in the insects, sediment and detritus, while there was no correlation between these concentrations and the concentration in surface water. Insect Se burden may therefore provide a more accurate measurement of food web accumulation risk than surface water Se concentration. The importance of organism-specific factors on Se transfer to higher trophic levels was revealed by the steady-state Se body burden within the same insect taxa occupying similar environmental compartments in both aquatic systems. Additionally, however, insect Se body burdens, even within similar taxa, were up to 7 times greater within the lentic compared with the lotic system, and site-specific biogeochemical processes are also likely to play a role in the pattern and level of Se accumulation between hydrogeochemically different aquatic systems occurring within the same watershed. Though a site-specific relationship was apparent between organic content and sediment and detritus Se concentrations, this factor did not account for insect Se accumulation differences between the lotic and lentic aquatic habitats. If carbon content is to be used as a site-specific predictor of Se accumulation potential, further investigations of it's influence on the food web accumulation rate of Se are required.