The Myakka and Peace River Basins constitute more than 60 percent of the total inflow area and contribute more than half the total tributary inflow to the Charlotte Harbor estuarine system. Water discharge and nutrient enrichment have been identified as significant concerns in the estuary, and consequently, it is important to accurately estimate the magnitude of discharges and nutrient loads transported by inflows from both rivers. Two methods for estimating discharge and nutrient loads from tidally affected reaches of the Myakka and Peace Rivers were compared. The first method was a tidal-estimation method, in which discharge and nutrient loads were estimated based on stage, water-velocity, discharge, and water-quality data collected near the mouths of the rivers. The second method was a traditional basin-ratio method in which discharge and nutrient loads at the mouths were estimated from discharge and loads measured at upstream stations. Stage and water-velocity data were collected near the river mouths by submersible instruments, deployed in situ, and discharge measurements were made with an acoustic Doppler current profiler. The data collected near the mouths of the Myakka River and Peace River were filtered, using a low-pass filter, to remove daily mixed-tide effects with periods less than about 2 days. The filtered data from near the river mouths were used to calculate daily mean discharge and nutrient loads. These tidal-estimation-method values were then compared to the basin-ratio-method values. Four separate 30-day periods of differing streamflow conditions were chosen for monitoring and comparison. Discharge and nutrient load estimates computed from the tidal-estimation and basin-ratio methods were most similar during high-flow periods. However, during high flow, the values computed from the tidal-estimation method for the Myakka and Peace Rivers were consistently lower than the values computed from the basin-ratio method. There were substantial differences between discharges and nutrient loads computed from the tidal-estimation and basin-ratio methods during low-flow periods. Furthermore, the differences between the methods were not consistent. Discharges and nutrient loads computed from the tidal-estimation method for the Myakka River were higher than those computed from the basin-ratio method, whereas discharges and nutrients loads computed by the tidal-estimation method for the Peace River were not only lower than those computed from the basin-ratio method, but they actually reflected a negative, or upstream, net movement. Short-term tidal measurement results should be used with caution, because antecedent conditions can influence the discharge and nutrient loads. Continuous tidal data collected over a 1- or 2-year period would be necessary to more accurately estimate the tidally affected discharge and nutrient loads for the Myakka and Peace River Basins.