Regular consumption of seafood and, in particular, fish has been associated with important health benefits. A fish product that has been increasingly included in the human nutrition is roe. Despite its nutritional value has been established (fatty acid profile and protein content), the knowledge of the composition of its aqueous extracts is still limited. This work describes the bioactive compounds profile in the roe-derived aqueous extracts of three different marine species (sardine, horse mackerel and sea bass) using a method based on liquid chromatography coupled to high-resolution mass spectrometry with an electrospray ionisation source (LC-ESI/HRMS). The presence of substances with well-known nutritional and functional properties (e.g., antioxidant and anti-inflammatory properties) was demonstrated, namely essential amino acids (e.g., taurine), peptides (e.g., anserine and carnosine), B-group vitamins (e.g., nicotinamide) and gadusol. Therefore, roe-derived aqueous extracts are excellent sources of bioactive compounds and may be used as a font of functional components for several medical and veterinary applications.