Native freshwater mussels can influence the aquatic N cycle, but the mechanisms and magnitude of this effect are not fully understood. We assessed the effects of Amblema plicata and Lampsilis cardium on N transformations over 72 d in 4 continuous-flow mesocosms, with 2 replicates of 2 treatments (mesocosms with and without mussels), equipped with electronic water-chemistry sensors. We compared sensor data to discrete sample data to assess the effect of additional sensor measurements on the ability to detect mussel-related effects on NO3– formation. Analysis of 624 sensor-based data points detected a nearly 6% increase in NO3– concentration in overlying water of mesocosms with mussels relative to mesocosms without mussels (p < 0.05), whereas analysis of 36 discrete samples showed no statistical difference in NO3– between treatments. Mussels also significantly increased NO2– concentrations in the overlying water, but no significant difference in total N was observed. We used the sensor data for phytoplankton-N and NH4+ to infer that digestion times in mussels were 13 ± 6 h. The results suggest that rapid increases in phytoplankton-N levels in the overlying water can lead to decreased lag times between phytoplankton-N and NH4+ maxima. This result indicates that mussels may adjust their digestion rates in response to increased levels of food. The adjustment in digestion time suggests that mussels have a strong response to food availability that can disrupt typical circadian rhythms. Use of sensor data to measure directly and to infer mussel effects on aquatic N transformations at the mesocosm scale could be useful at larger scales in the future.