Biodiversity is a multifaceted concept, yet most biodiversity studies have taken a taxonomic approach, implying that all species are equally important. However, species do not contribute equally to ecosystem processes and differ markedly in their responses to changing environments. This recognition has led to the exploration of other components of biodiversity, notably the diversity of ecologically important traits. Recent studies taking into account both taxonomic and trait diversity have revealed that the two biodiversity components may exhibit pronounced temporal and spatial differences. These apparent incongruences indicate that the two components may respond differently to environmental drivers and that changes in one component might not affect the other. Such incongruences may provide insight into the structuring of communities through community assembly processes, and the resilience of ecosystems to change. Here we examine temporal and spatial patterns and drivers of multiple marine biodiversity indicators using the North Sea fish community as a case study. Based on long-term spatially resolved survey data on fish species occurrences and biomasses from 1983 to 2014 and an extensive trait dataset we: (i) investigate temporal and spatial incongruences between taxonomy and trait-based indicators of both richness and evenness; (ii) examine the underlying environmental drivers and, (iii) interpret the results in the context of assembly rules acting on community composition. Our study shows that taxonomy and trait-based biodiversity indicators differ in time and space and that these differences are correlated to natural and anthropogenic drivers, notably temperature, depth and substrate richness. Our findings show that trait-based biodiversity indicators add information regarding community composition and ecosystem structure compared to and in conjunction with taxonomy-based indicators. These results emphasize the importance of examining and monitoring multiple indicators of biodiversity in ecological studies as well as for conservation and ecosystem-based management purposes.