The search for extraterrestrial bio-signatures and the origin of Earth’s water remain two of the most compelling questions in planetary science. While no direct evidence of life beyond Earth has been found, water is a key prerequisite for life, and tracing its presence throughout the solar system may provide vital clues. A leading theory suggests that Earth’s water may have originated from comets, supported by limited water isotopic measurements that match Earth’s ocean water. However, more data from a larger sample of comets is needed to validate this theory. Traditional sub-millimeter wave spectrometers, capable of such measurements, are often too large and power-intensive for small spacecraft platforms. To address this, we present WHATSUP—a next-generation, ultra-compact, low-power, room-temperature submillimeter-wave (500-600 GHz) spectrometer—designed primarily for CubeSat and SmallSat platforms, though equally well-suited for a range of other missions. WHATSUP utilizes advances in CMOS system-on-chip electronics, innovative low profile and low mass silicon lens antenna, Micro-electro mechanical system (MEMS)-based THz switching, and a novel programmable calibration load. Together, these innovations deliver a highly integrated system with a total mass of only 2 kg and power consumption under 7 W, which is a substantial improvement over previous submillimeter-wave instruments. This enables affordable, high-frequency spectral observations from multiple low-cost missions, potentially revolutionizing how isotopic studies of cometary water are conducted and opening new pathways for outer solar system exploration. WHATSUP instrument was flown on the NASA Hand Launch Payload (HLP) ballooncraft and performed atmospheric soundings across Texas, USA in July 2023.