Recent studies from both freshwater and marine habitats highlight the potential for estimation of biogeochemical processes, particularly autotrophic assimilation, from diel variation in nutrients such as nitrate. However, these approaches have been developed and applied to systems (productive oceans and spring-fed rivers) ideally suited to their use. I will review the findings of these studies to illustrate the kinds of inference that are already being drawn, and then address our efforts to extend the range of systems, solutes, and circumstances under which these approaches can be used. Laboratory experiments demonstrate the capabilities of commercially available nitrate sensors to detect diel variation as small as 7 µ g NO3-N L-1 , and the minimal interference by colored dissolved organic matter under all but the highest concentrations (>10 mg DOC L-1). We use these data to bound the ranges of discharge and productivity that should permit estimation of autotrophic assimilation using existing methods in lotic and lentic systems. We also introduce a two-station approach that allows inference of autotrophic assimilation against dynamic inputs from terrestrial systems. Our results suggest that estimation of autotrophic assimilation from diel variation may be possible in a wide range of aquatic environments, but that the strongest inference about biogeochemical processes will require a combination of approaches.