Abstract Portable in situ ultraviolet-visual spectrometers, through high frequency water quality measurements, provide new insight into biogeochemical processes occurring within dynamic ecosystems. Nitrogen and carbon cycling were observed in two distinct wetland mesocosm environments during a two-year mesocosm study. Simulated drainage water was loaded into the mesocosms across seasons with target nitrate-N levels between 2.5 and 10 mg L−1. Nitrate-N and dissolved organic carbon concentrations in the water column were measured hourly with the spectrometer and calibrated with water quality grab samples. Prominent and unique diel cycles were observed in both nitrate-N and dissolved organic carbon readings from the spectrometer, which reveal biogeochemical processes in these systems are more complicated than typically considered in empirical models. Findings support the importance of utilizing high frequency monitoring to advance current knowledge of nitrogen and carbon processes occurring in treatment wetland ecosystems.