Neodermopthirius harkemai is an ectoparasitic flatworm of Lemon Sharks (Negaprion brevirostris) that causes hemorrhagic skin lesions and can persist in saltwater aquaria by spreading via swimming larvae and eggs. Although first described morphologically in 1963, no genome or rDNA sequence data exist, limiting molecular detection and accurate classification. Here, we present the first draft genome of N. harkemai and evaluate its detectability in aquarium water before, during, and after antiparasitic treatment. Adult parasites were collected from two infected sharks, and whole-genome sequencing was performed using Illumina NovaSeqX (~100M read pairs). After assembly, contaminant contigs were removed to generate a draft genome of ~350 Mb. Aquarium water was sampled at three timepoints relative to praziquantel treatment. Two-liter samples were filtered through 0.1 µm and 40 µm filters, DNA was extracted, and 20M read pairs per sample were sequenced. Microbial community analysis was performed using Sourmash. Metagenomic analysis revealed that 40 µm filters captured the greatest microbial eukaryote diversity, whereas prokaryotes dominated across all samples. Fifteen Vibrio species were detected, including potential pathogens (V. fortis, V. jasicida), as well as unculturable bacteria such as Neptunochlamydia vexilliferae, an endosymbiont of marine amoebae. N. harkemai DNA was detectable in water samples, and signal dynamics corresponded with treatment timing. This work provides the first genomic resource for N. harkemai and demonstrates the utility of metagenomics for parasite detection in aquaria. Unexpected microbial diversity observed suggests that saltwater aquaria may serve as microcosms reflecting broader marine microbial ecosystems, offering insights into host-parasite-microbe interactions.