The analysis of lipid disruption in invertebrates is limited by our poor knowledge of their lipidomes and of the associated metabolic pathways. For example, the mechanism by which exposure of the crustacean Daphnia magna to tributyltin, juvenoids, or bisphenol A increase the accumulation of storage lipids into lipid droplets is largely unknown/presently unclear. Here we analyze transcriptome changes subsequent to this lipid accumulation effect induced by either the pesticide pyriproxyfen (a juvenoid agonist), the plasticizer bisphenol A, or the antifouling agent tributyltin. Changes in the whole transcriptome were assessed after 8 and 24 h of exposure, the period showing the greatest variation in storage lipid accumulation. The three compounds affected similarly to a total of 1388 genes (965 overexpressed and 423 underexpressed transcripts), but only after 24 h of exposure. In addition, 225 transcripts became up-regulated in samples exposed to tributyltin for both 8 h and 24 h. Using D. melanogaster functional annotation, we determined that upregulated genes were enriched in members of KEGG modules implicated in fatty acid, glycerophospholipid, and glycerolipid metabolic pathways, as well as in genes related to membrane constituents and to chitin and cuticle metabolic pathways. Conversely, down-regulated genes appeared mainly related to visual perception and to oocyte development signaling pathways. Many tributyltin specifically upregulated genes were related to neuro-active ligand receptor interaction signaling pathways. These changes were consistent with the phetotypic effects reported in this and in previous studies that exposure of D. magna to the tested compounds increased lipid accumulation and reduced egg quantity and quality.