This article investigates several variants of noncoherent multiple-frequency-shift keying (MFSK) that uses Polar coding and evaluates their applicability to robust underwater acoustic underwater communication. A simplified data model is assumed, yielding a low-complexity MFSK symbol estimator, and symbol likelihoods are calculated using sparse pilot symbols. Results presented from field tests in the Stockholm archipelago indicate that a Polar code will decode with a low frame error rate (FER) if not signal-to-noise ratio (SNR) limited and that its performance is superior to convolutional coding. The reliability of short frames, with 0.16–0.5 s transmission time, and long frames, with spectral efficiency up to 0.1 b/s/Hz, are evaluated in the five replay channels of the Watermark benchmark over varying SNR and SNR per bit, <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$E_{b}/N_{0}$</tex-math></inline-formula> . Synchronization is solved with a sliding hypothesis approach and the results show a FER <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\lesssim 1 \%$</tex-math></inline-formula> for <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">all</i> Watermark channels, where the robustness is significantly improved by either increasing the frequency separation of tones or lowering the code rate and extending the frame length. The performance compares favorably to methods found in the literature, particularly for the less-benign channels of the benchmark.