Transcriptomes of twelve freshwater pennate diatom at three pH conditions: acidic (4.7), neutral (7.0) and alkaline (8.2). Species were isolated from Pyrenean lake samples (Spain) by single-cell pipetting, and populations were grown in a common garden involving three pH conditions. Each strain and pH condition has three replicates. Each ENA experiment includes one replicate. ENA experiment labeling: "[strain name][pH condition][replicate]". pH condition: "pH4" for pH 4.7, "pH7" for pH 7.0, "pH8" for pH 8.2. Replicate: "repA" for replicate A, "repB" for replicate B, "repC" for replicate C.