Hydroponic Cropping Systems (HCS) including hydroponics and aquaponics are becoming increasingly popular as a solution to address global food security. Plants are grown hydroponically under controlled environments and are considered to have fewer food safety concerns than traditional field farming. However, HCS might have very different sources of microbial food safety risks that are under-examined. Here, we investigated the microbiomes, microbial hazards, and the bacterial transmission route of hydroponic and aquaponic ecosystems using high-throughput 16S-ITS-23S rRNA gene sequencing and bioinformatic approaches together with a food safety practice survey. Especially, the 16S-ITS-23S rRNA sequencing with ASV taxonomy assignment allows us to achieve a higher sequencing resolution and recognize the presence of spoilage microorganisms and potential human, plant, and fish pathogens in the systems. With the SourceTracker and overlapping ASVs, we predicted the transmission route to be by-direction and constructed the bacteria transmission map, which can be implemented in future food safety risk control plans. The potential risks at both types of farms were associated with hygiene practices of personnel and equipment. Our study provides insight into microbial hazards investigation without targeting specific foodborne pathogens.