Wetlands along upper estuaries are characterized by dynamic transitions between forested and herbaceous communities (marsh) as salinity, hydroperiod, and nutrients change. The importance of belowground net primary productivity (BNPP) associated with fine and coarse root growth also changes but remains the dominant component of overall productivity in these important blue carbon wetlands. Appropriate BNPP assessment techniques to use in various tidal wetlands are not well-defined, and could make a difference in BNPP estimation. We hypothesized that different BNPP techniques applied among tidal wetlands differ in estimation of BNPP and possibly also correlate differently with porewater nutrient concentrations. We compare 6-month and 12-month root ingrowth, serial soil coring techniques utilizing two different calculations, and a mass balance approach (TBCA, Total Belowground Carbon Allocation) among four tidal wetland types along each of two river systems transitioning from freshwater forest to marsh. Median values of BNPP were 266 to 2946 g/m2/year among all techniques used, with lower BNPP estimation from root ingrowth cores and TBCA (266–416 g/m2/year), and higher BNPP estimation from serial coring of standing crop root biomass (using Smalley and Max-Min calculation methods) (2336–2946 g/m2/year). Root turnover (or longevity) to a soil depth of 30 cm was 2.2/year (1.3 years), 2.7/year (1.1 years), 4.5/year (0.9 years), and 1.2/year (2.6 years), respectively, for Upper Forest, Middle Forest, Lower Forest, and Marsh. Marsh had greater root biomass and BNPP, with slower root turnover (greater root longevity) versus forested wetlands. Soil porewater concentrations of NH3 and reactive phosphorus stimulated BNPP in the marsh when assessed with short-deployment BNPP techniques, indicating that pulses of mineralized nutrients may stimulate BNPP to facilitate marsh replacement of forested wetlands. Overall, ingrowth techniques appeared to represent forested wetland BNPP adequately, while serial coring may be necessary to represent herbaceous plant BNPP from rhizomes as marshes replace forested wetlands.