We assess the trends and influences of non-indigenous and cryptogenic species (hereafter simply referred to as “NIS”) on Danish marine community compositions using three decades of quantitative monitoring data. Since the initiation of the Danish marine monitoring programmes in the 1980s, the number of marine NIS recorded in Denmark increased from 30 to 77 in 2014. Thus, of the total 77 marine NIS known from Denmark, 56 (73%) were captured in the standardized monitoring program, while the remaining 21 species (27%) were not detected (in particular gelatinous zooplankton, shallow water fish, parasitic invertebrates, and littoral angiosperms) because of limited spatial-temporal sampling efforts as well as methodological limitations. Significant exponential increases in records of non-native phytoplankton, benthic invertebrates and macroalgae (only in one region) relative to the total species records in the database were observed. Multivariate analyses of presence-absence data, indicated that the contribution of NIS to total community similarity increased over time, highlighting that NIS is becoming an increasingly important component of Danish marine communities. While the presence of NIS generally explained less than 10% of long-term changes in the community similarity across large regions, NIS presence showed local dominance. A correlation analysis indicated that changes in overall species composition within functional groups (phytoplankton, zooplankton, macroalgae and benthic fauna) were related to changes in NIS contribution but more strongly influenced by salinity, highlighting a well-described general positive relationship between salinity and species richness in Danish waters. The process described within this study could form the basis for the analysis of impact of NIS in marine water as required by the Marine Strategy Framework Directive (MSFD).