A critical determinant of the effective denitrification potential in karst aquifers is the relative contribution of matrix and non-matrix (e.g., conduits) to the total groundwater flow. This work tests the hypothesis that observed karst aquifer-scale denitrification rates represent the superposition of the effects from matrix zones, which have low denitrification rates and long residence times, and non-matrix zones, which have higher denitrification rates and short residence times. To better evaluate karst whole-aquifer denitrification capacity, this study examined groundwater chemical data from 69 individual wells across the springshed of Silver Springs, FL, and conducted five push–pull tracer tests (PPTTs) in matrix and non-matrix aquifer sections. Mean residence times and mean zero-order denitrification rates (K0) were determined using reduced-complexity analytical models for matrix and non-matrix zones. Significant nitrate degradation at the local scale was observed in wells that sampled matrix portions of the aquifer (K0 ≈ 5 to 7 × 103 μmol N/L/d), indicating denitrification hotspots comparable to previous results employing the same PPTT method. However, PPTTs in matrix portions of the aquifer found no evidence of aquifer denitrification, likely due to the short residence times experienced during PPTTs. The analytical models coupled with the measured nitrate concentrations and excess N2 data in groundwater discharged at the spring vents showed whole-aquifer estimates of residence times tavg = 4.2 years and aquifer denitrification rate K0,avg = 0.01 ± 0.01 μmol N/L/d that were consistent with previous studies. However, the average denitrification rate for non-matrix zones K0,nm = 1.29 ± 0.92 μmol N/L/d was two orders of magnitude higher than that for matrix zones K0,m = 0.002 ± 0.001 μmol N/L/d. Whole-aquifer denitrification measures thus reflect the weighted contributions of low denitrification in non-matrix zones, which constitute the majority of the groundwater flow, and high-denitrification but low-flow matrix zones. The modeling approach with non-matrix networks from this study can provide insight into the catchment-scale N budget and transport in karst aquifers.