<p>Protected areas (PAs) are crucial for biodiversity conservation, yet aquatic ecosystems often receive less attention. Meiofauna plays a key role in aquatic ecology, and changes in its community structure are valuable indicators of environmental quality, highlighting its growing relevance for conservation. This review aimed to: (1) analyze trends in meiofaunal community structure within marine and freshwater protected ecosystems; (2) evaluate the global state of knowledge on meiofauna in PAs; and (3) identify research gaps and propose future directions. The PRISMA protocol was used. Of 213 articles screened, 52 met the inclusion criteria, with most studies conducted in temperate regions. Meiofaunal communities were strongly shaped by habitat complexity, sediment characteristics, organic matter inputs, hydrological gradients, sea level rise, and anthropic pressures. Protected areas generally supported higher diversity, functional richness, and evidence of ecological recovery. Major gaps include the lack of standardized mesh sizes in meiofauna sampling and the scarce inclusion of detailed protected areas management plan information. Future research should prioritize identifying appropriate seasonal windows for sampling to reduce bias. Strengthening these foundations will enhance the use of meiofauna as an indicator of ecosystem condition and improve the effectiveness of monitoring and conservation programs in protected areas.</p>