Environmental DNA (eDNA) metabarcoding is revolutionizing biodiversity monitoring, but comparisons against traditional data are uncommon. We targeted eukaryotes through the 18S barcode amplified from water samples at 20 sites from the Gulf of California (GC), and contrasted eDNA against 316 simultaneous visual surveys and a historical database with over 5k species. From 61k Amplified Sequence Variants, we identified 850 eukaryotic families, of which half represent new compiled records, including 174 families of planktonic, benthic, and parasitic invertebrates. eDNA revealed many overseen taxa, highlighting higher taxonomic ranks within micro invertebrates, microscopic fungi, and other micro eukaryotes from the supergroups Stramenopiles, Alveolata, and Rhizaria. The database combining all methods has doubled the number of distinct phyla, classes and orders compared to the historical baseline, indicating biodiversity levels in the GC are much higher than previously assumed. The estimated proportion of historical taxa included in public reference databases was only 18% for species, explaining the small portion of eDNA reads that were taxonomically assigned to species level (13%). Each method showed different taxonomic biases, with eDNA missing vertebrates, visual surveys targeting only seven phyla, and the historical records focusing on macroinvertebrates, fish and algae. Although all methods recovered the main known biogeographic regionalization, eDNA data did not support the historical pattern of higher diversity in the Central than Northern GC. While combining methods provides a novel view of biodiversity that is much more comprehensive than any individual approach, our study highlights many challenges in synthesizing biodiversity data from traditional and novel sources.