The effect of proton exchange on the measurement of1H–1H,1H–2H, and2H–2H residual dipolar interactions in water molecules in bovine Achilles tendons was investigated using double-quantum-filtered (DQF) NMR and new pulse sequences based on heteronuclear and homonuclear multiple-quantum filtering (MQF). Derivation of theoretical expressions for these techniques allowed evaluation of the1H–1H and1H–2H residual dipolar interactions and the proton exchange rate at a temperature of 24°C and above, where no dipolar splitting is evident. The values obtained for these parameters at 24°C were 300 and 50 Hz and 3000 s−1, respectively. The results for the residual dipolar interactions were verified by repeating the above measurements at a temperature of 1.5°C, where the spectra of the H2O molecules were well resolved, so that the1H–1H dipolar interaction could be determined directly from the observed splitting. Analysis of the MQF experiments at 1.5°C, where the proton exchange was in the intermediate regime for the1H–2H dipolar interaction, confirmed the result obtained at 24°C for this interaction. A strong dependence of the intensities of the MQF signals on the proton exchange rate, in the intermediate and the fast exchange regimes, was observed and theoretically interpreted. This leads to the conclusion that the MQF techniques are mostly useful for tissues where the residual dipolar interaction is not significantly smaller than the proton exchange rate. Dependence of the relaxation times and signal intensities of the MQF experiments on the orientation of the tendon with respect to the magnetic field was observed and analyzed. One of the results of the theoretical analysis is that, in the fast exchange regime, the signal decay rates in the MQF experiments as well as in the spin echo or CPMG pulse sequences (T2) depend on the orientation as the square of the second-rank Legendre polynomial.