Sandy beaches are important ecosystems providing coastal protection and recreation, but they face significant threats from human activities and sea level rise. They are inhabited by meiofauna, small benthic invertebrates that are highly abundant and diverse, but are commonly understudied biotic components of beach ecosystems. Here, we investigate the factors shaping meiofaunal metacommunities by employing Generalised Dissimilarity Modelling (GDM) and Joint Species Distribution Modelling (JSDM) to study community turnover and assembly processes. We analysed over 550 meiofauna samples from a >650 km stretch of the southern North Sea coastline using a metabarcoding approach. Our findings reveal that environmental factors, especially Distance from Low Tide and Sediment Grain Size, are important drivers of meiofauna community turnover. This highlights the influence of the gradient from marine to terrestrial habitats and sediment conditions. Spatial factors, which indicate dispersal limitations, also significantly impact community composition, challenging the view that marine meiofauna have broad geographic distributions. The JSDM results show that species sorting by environmental conditions is the dominant process in community assembly with increasing environmental differences between sampling sites, but that biotic associations, or similar environmental preferences, are a major driver of community assembly at sites with similar environmental conditions. Further, we find that spatial factors also significantly influence community assembly across the study region. By facilitating the inference of ecological niches for a high number of meiofaunal taxa, JSDM provides a powerful framework for understanding the ecology of these animals. Our results highlight the importance of considering environmental gradients and dispersal limitations in meiofauna and beach ecosystem research, and future research should aim at adding information on functional traits and biotic interactions under varying environmental conditions to understand meiofauna community dynamics and resilience.