We present a comparison of four different methods of measuring sensible (H) and latent (LE) heat fluxes for a year over a mixed grass prairie ecosystem in the Nebraska SandHills [eddy covariance (EC), energy balance/Bowen ratio (EBBR), residual energy (RES), modified Bowen ratio (MBR) methods]. Additionally, we developed a set of quality control criteria for each method and present a simplification to the traditional EBBR setup. Using EC as reference, all methods yielded similar estimates of yearly H (regression slopes (m) ~ 2% from unity; HEC > HEBBR, HRES, and HMBR). For yearly LE, EBBR and RES yielded similar estimates with EC (m ~ 2% from unity; LEEC < LEEBBR and LERES), while a larger bias was found from MBR (m ~ 8% from unity; LEEC > LEMBR). At shorter time scales (~ hourly), moderate scatter was found about linear regression fits for H between EBBR and EC (R2 = 0.81), with smaller scatter between RES and MBR, and EC (R2 = 0.91). For LE, smaller scatter was also measured between EC, and EBBR and RES (R2 = 0.89 and 0.87, respectively), with the larger scatter between EC and MBR (R2 = 0.65). This suggests methods other than EC may be well suited to longer-term applications (≥ yearly), but have larger uncertainty on individual measurements.