Intracavitary atrial electrograms (EGMs) provide high-resolution insights into cardiac electrophysiology but are often contaminated by noise and remain high-dimensional, limiting real-time analysis. We introduce CLARAE (CLArity-preserving Reconstruction AutoEncoder), a one-dimensional encoder--decoder designed for atrial EGMs, which achieves both high-fidelity reconstruction and a compact 64-dimensional latent representation. CLARAE is designed to preserve waveform morphology, mitigate reconstruction artifacts, and produce interpretable embeddings through three principles: downsampling with pooling, a hybrid interpolation--convolution upsampling path, and a bounded latent space. We evaluated CLARAE on 495,731 EGM segments (unipolar and bipolar) from 29 patients across three rhythm types (AF, SR300, SR600). Performance was benchmarked against six state-of-the-art autoencoders using reconstruction metrics, rhythm classification, and robustness across signal-to-noise ratios from -5 to 15 dB. In downstream rhythm classification, CLARAE achieved F1-scores above 0.97 for all rhythm types, and its latent space showed clear clustering by rhythm. In denoising tasks, it consistently ranked among the top performers for both unipolar and bipolar signals. In order to promote reproducibility and enhance accessibility, we offer an interactive web-based application. This platform enables users to explore pre-trained CLARAE models, visualize the reconstructions, and compute metrics in real time. Overall, CLARAE combines robust denoising with compact, discriminative representations, offering a practical foundation for clinical workflows such as rhythm discrimination, signal quality assessment, and real-time mapping.